I have a similar question.. the class for me is not a pre-req, it's an art history class. However I graduated from college and finished that class nearly 5 years ago. If i were to retake that class, it would still be on my college transcript. but would it still show up when calculated for a MD program>?
If you did poorly in a prerequisite, you should take it again. There are stories of success with poor grades on their transcripts (I know a successful ER doc who told me he got a D in Orgo), but these people are rare. My advice is to take this course again.
If the course is not a pre-req and some time has elapsed, leave it be. You prove your mettle by acing your pre-reqs and demonstrating success in the nearer term. I had some poor non pre-req grades on my undergrad transcript from freshman year. When I applied to medical school at age 35 it didn't seem to matter.