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. 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 Kor-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.