i don't think it matters that much. honors is defined differently at different schools so it's difficult for med schools to gauge how much more rigorous an honors program is compared to the non-honors program at the same school.
unless you really really really want the honors diploma from your university, i'd stay out of it, do exceptionally well in the non-honors track, and have an easy time getting into med school. anyone with a 3.8+ GPA and 30+ MCAT has an exceedingly high chance of getting into medical school over someone who has a 3.5 GPA and 30+ MCAT with an honors diploma.