Teachers at my school are explicitly told not to give a bad reference. Instead, they just focus on what you're good at and let the admissions tutors read between the lines. In your case, for example, your teachers probably wouldn't write anything about your contributions to the class. That way they're not lying and the admissions tutor might be able to figure out that since it's not written about, you don't make lots of contributions to the class.
I really wouldn't worry about it though, they won't paint you in a bad light unless you're a particularly awful student. However, if I were you I would take those comments on board and try to contribute more to the class next year. At university you'll be in smaller groups (especially if you're going to a uni which practices the PBL learning style) so you won't be able to get away with not joining in discussion. Ability to communicate is key to studying medicine and is something admissions tutors look for (as I'm sure you know) so take from that what you will.