If you think you can leave amicably and get a good LOR, leave. If you think your PI is the type who might refuse to write you a letter/write a crappy one if you leave, unfortunately staying might be a better idea. The main thing for the LOR is to maintain a good relationship with your PI, and if you don't have that/don't see yourself able to maintain that because of how it is in the lab, leaving and considering other options for a LOR is best.
I wouldn't worry about med schools asking too many questions about your research since you're an MD-only applicant, and they certainly don't expect you to do research every single semester. If you just joined this lab and leave now, there may be questions about why you left so quickly, and you might not be able to significantly talk about the research that you've done. But if you've been there for a while and can talk about what you did, there's nothing to worry about with respect to the med schools. Very few med schools asked me about my research at interviews, and focused more on my clinical experiences (as an MD-only applicant), but that's my n=1 experience.