Depends on how strong her letter is and what type of schools you're applying to. If you're applying to big research schools, I think it will help to have a strong letter from a PI to back up the research experience you list on your application; with more community/clinically focused schools, I think it would matter less.
If you have another option, I would go with that - it's better to have letter writers who really want to help you get into medical school, not just those who will write a routine letter.
If you do end up asking, just ask her if she would be comfortable to write you a STRONG letter of recommendation. I think most people realize that a negative/neutral letter can sink an otherwise strong application, and would tell you that they can't write a strong letter. If she says no or even hesitates when you ask, then you can walk away knowing you tried.
Edit: Also, if you made friends with any of the grad students in the lab, maybe ask them what their impression was - maybe your PI is just awkward and comes off as unfriendly without meaning it. Just a thought.