Here's the lesson I've learned from my application process. Med schools care more about a high GPA than anything else. If you do the honors program, you'd better damn well make sure you can get an A in every class. As someone already posted above, "treat your GPA with kid-gloves." Right now, you're still in this high-school mentality of "Go above and beyond" and "challenge" yourself. But the catch is that you've also gotta ace those classes. In high school, I was the go-getter, all AP student, etc, etc. And so my first year in college, I was like, "oh, I got into Honors Calculus? Okay, i'll take that. Oh there's an honors biology class? Okay I'll take that." I ended up with mediocre grades-- I learned a buttload, mind you-- but with the extreme grade deflation, it didn't translate to A's. If I could do it all over again, I would either step down to regular classes, or work 10 times as hard to get an A.
So just keep that in mind-- that you've still got to get A's. Don't try to excuse it with "Oh it's an honors class, so a B is just as good." Not to the Medical Admssions Committees.
On a side note-- I can't give enough praise to small class sizes. That alone might convince me to take the honors route. Also, small class-sizes = more personal attention from profs= better recommendation letters.
Ah, hindsight is always 20/20!!