For this reason I always let the game run for 10-15 seconds before I profile, figuring that by that time most of the opt/deopt churn will be finished. And this (very useful) script seems to back this up - I get output like yours at startup, but if I wait a while and then rm the output files, further output is relatively minimal.
So I'm inclined to think that opt/deopt stuff isn't the issue, and there really are lots of JS heap objects getting allocated somewhere. At the same time though, when I used Chrome's built-in memory profiling I see a bunch of deopt-related strings, so maybe I'm way off base. If anyone sees what I'm missing please do clue me in.
(Also: great tip on the script!)