Kro-necker versus Kron-ecker: which hyphenation is preferred? Synopsis and concrete practices
Everyone is thanked for their comments, and in view of the diversity of views expressed, I have converted this question to a community wiki.
Here is a working synopsis:


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*With regard to the alternative hyphenations Kron-ecker versus Kro-necker, the "advanced search" feature of Google Books establishes that both hyphenations are in common usage.  

*The rules of German-language orthography are sufficiently intricate, and the etymology of the name Kronecker is sufficiently obscure, as to provide well-founded justifications for either hyphenation.

*No one has come forth with a set of standardized hyphenations for mathematician's names that is in-use by a major mathematical journal or publishing house.
In light of the preceding findings, one reasonable practice is the following:


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*Include in the LaTex preamble a list of problematic mathematician's names that (by default) forbids their hyphenation (this was Theo Johnson-Freyd's excellent recommendation):
      \hyphenation{Kronecker Riemann Spivak}

*Upon the (rare) occasions that acceptable typography requires hyphenation of one of these names, then in the body of the manuscript optional hyphens can be inserted in the LaTeX file: 
      \LaTeX optionally hyphenates Kron\-ecker Rie\-mann Spi\-vak

*In placing optional hyphens, lend equal weight to common usage and correct orthography (recognizing that these can be ambiguous upon occasion).  

*Search methods help resolve problematic cases, for example the hyphenation Rie-mann is overwhelmingly preferred over Riem-ann.
And finally, we should all remember to be grateful to Donald Knuth, who gave us the wonderful tools that allow us to balance good orthography with good typography. 

Original question
The question asked is:

Kro-necker versus Kron-ecker: which hyphenation is preferred?

Equivalently, in TeX/LaTeX should one include "\hyphenation{Kron-ecker}" in the preamble?  Or should one simply accept the default TeX/LaTeX hyphenation "Kro-necker"?
A search of the tex-hyphen archives provides neither guidance specifically on "Kronecker," nor general guidance on preferred hyphenations for mathematician's names (except to show that there is a community of people who care passionately about these lexicographical issues).
Therefore, instantly "accepted" will be any MathOverflow answer that provides a standardized "\hyphenation{...}" file (including mathematician's names) from any respected mathematical journal or publishing house.
Although this question is perhaps not the most important ever asked on MatherOverflow, such a preferred-hyphenation list would be welcomed by me, and (IMHO) by many mathematical writers.  For example, are there other problematic mathematical names?
Recognizing too that some folks are relatively indifferent to mathematical hyphenation, these folks can provide instruction and amusement by offering opinions on the question "Why has the usage of 'Kronecker' been increasing inexorably for the past fifty years?"
Google NGRAMS of Kronecker http://faculty.washington.edu/sidles/ENC_2011/Kronecker_usage.png
As Mark Twain might have put it:

Any calm person, who is not blind or idiotic, can see that in the year 52,011 or thereabouts, every book produced by human civilization will consist solely of the sentence "Kronecker, Kronecker, Kronecker,…"There is something fascinating about Google's Books Ngram Viewer.  One gets such wholesale returns of conjectures, out of such a trifling investment of fact.

However, any opinions offered in this regard, no matter how erudite or amusingly stated, will not be considered as answers.
 A: Kron-ecker, I would think, being a native speaker of German. Kron(e) is crown, Ecker alone is a not totally uncommon german name.  
A: Kro - necker since it matches the way the name is pronunced, which is something like KROW nek er , according to http://nsm1.nsm.iup.edu/gsstoudt/pronounce.html and my experience (native speaker German and 10+ years experience in native German math environment). 
More generally, I think this prunciation guide could be useful to decide such questions for other names.

ADDED: 
I leave my original answer unchanged, as otherwise the comments might not make sense after  the edit. I add some more explanation justifying the correctness, at least so I think, of my answer and expand it; however I might actually be the case that both answers are correct, but I am not sure, details below.
A disclaimer: I do not claim any expert knowledge on anything below, but after some reading I hope to get it about right. 
First, a general remark: German hyphenation rules were changed somewhat recently;
the general trend of this change is a desire for simplification and thus also hyphenation more along the lines of the 'breaks' of the spoken language. (This is not everything there is to it, but I do not want to go into all details; to be honest, I'd also have a hard time doing so.)
Still, as pointed out by Theo Buehler, it is/remains true that words that arise as a composition of other words, say two nouns or an added prefix are first to be hyphenated along this structural break and then the composing parts are broken up.
Often this is simple as it is clear how the word is build up, but sometimes it is not.
If the structure is not clearly visible (anymore) hyphenation along the spoken breaks is at least also correct. 
So, now what about Kronecker. It is no doubt true that 'Kron-' is a common prefix (to signal a relation to crown in the real and figurative sense), as documented by words like Kronprinz, Kronjuwelen, Kronleuchter; in all these cases the word without 'Kron' has a clear meaning and the 'Kron' modifies it. (This explains also, I'd say, why an automatic hyphenating program hyphenates there, it knows the prefix.)
However, I maintain that this does not mean that Kronecker should be treated like this, or at least it does not have to be treated like this, as it is a name whose origin is at least unclear and the common pronunciation suggestes that the origin is 'forgotten'. I can well imagine that the name originated in this way (as alluded to  by Thomas Geschke); note that Acker means field (in the agricultural sense), the plural is Äcker which is essentially homophonic to Ecker.
So, Kronecker might well have orginated in the way that a person was refered to the place of residence at/near the Kronacker or Kronäcker (the field(s) of the king).
In fact, Kronacker exists also as a name.
There might however also be other explanations for the name, though I agree they seem less plausible [Kroh and Krohn, the h is silent, are existing namens too; so Kronecker could also have developped as the Kroh(n) from Necker or Neckar; the latter are geographical names in Germany]; I don't know.
All I want to say is that the fact that Kronecker is  Kron+ecker is (if it is so at all) at least not clearly visible, and indeed blurred both by the spelling and by the pronunciation. 
Thus, it is at least admissible so hyphenate along the spoken break that is 
Kro-necker. It might also be correct to hyphenate Kron-ecker (but I do not know this).
Since we now discussed the first hyphenation point, now for the second though nobody asked for it: Krone-cker
This seems to contradict the pronunciation I gave at the start but not entirely so as the ck is a sort-of double k, and pronunciation is actually not far from Kro nek ker.
Indeed according to the old hyphenation rules I learned in school one would have hyphenated a word like 'backen' as bak-ken [c becomes k]; yet there might have been an exception for proper names. Yet by the new rules one hyphenates ba-cken. And, in analogy so Krone-cker.
To sum it up: Kro-ne-cker is I believe correct; perhaps also Kron-ecker (perhaps it is even more correct).
So, to answer the equivalent formulation of the question:
I would not change the default behavior of LaTeX, as the default is at least also correct. 
A: Cute question.  That said, I think that a good strategy might be that you should not allow any hyphenation of "Kronecker".  It would be very confusing for any reader to go along and hear about the Kro-
necker delta matrix, and it would also be confusing to be explained that the Kron-
ecker product of matrices is simply their exterior product.
A better approach is the following.  Do not worry about things like line breaks until you have completely completed the draft of the paper.  Then, at the end, yes, you should go back through and correct bad breaks by hand.  Sometimes this means that you should force LaTeX to fit more or less than it wants to in a line.  More often, it means that you should rewrite one sentence somewhere to avoid a bad hyphenation.
When you do submit to a journal, they may impose a house style.  But you will have a chance at the end to go over the proofs, and you can at that time do a similar one-word-rewrite to fix bad hyphenation.
(I have marked my answer as Community Wiki because, although I think this question is cute, I don't think it's the type of question for which answers should accrue "reputation points".  That said, marking the answer CW has the side effect of inviting edits to the answer.  So, just to emphasize: by all means please improve ("wiki") this answer, provided you do not change the basic thrust of the answer; if you wish to disagree, post a different answer.)
A: Kronecker is almost certainly derived from a place name, Kroneck. Krone means crown, and Eck means corner, this ending is frequently used for names of castles. Therefore the hyphenation should definitely be Kron-ecker.
Edit: Apparently a reform in the late 1990s changed the rules. If I understand it correctly, both hyphenations are now permissible.
