Mazur gives the following beautiful justification, which explains the “syn-” in “syntomic” as well.
Dear Thanos,
Thanks for your question. I'm thinking of “ local complete intersection” as being a way of cutting out a (sub-) space from an ambient surrounding space; the fact that it is flat over the parameter space means that each such "cutting" as you move along the parameter space, is---more or less---cut out similarly. I'm also thinking of the word "syntomic" as built from the verb temnein (i.e., to cut) and the prefix "syn" which I take in the sense of "same" or "together". So I think it fits.
Best wishes,
Barry

