It would seem that these MDs have very inflated egos, which may or may not be founded in reality. Some people tend to spend too much time in their bubbles. It's not uncommon for PI LORs to boast about their own accomplishments and mention how they personally (as if) were responsible for sending prior mentees to "top schools" and the like. Many write as if they are widely recognized, but quite frankly, are unknown to most/all on the adcom. So I do question whether they are as influential as they purport to be. Also, at my school, we rarely reach out to contacts during the decision-making stage.
For the vast majority of schools, you get to choose who you get letters from (Harvard being one exception that wants a letter from every research experience). In some cases (such as yours) where an applicant has a prolific research experience that yielded multiple publications, it can appear odd to not have a letter from that research mentor. When this apparent lack of a PI letter is brought up, it is sometimes a sticking point for some adcom members, whereas it is given a pass by others. In your case, I think that having a strong research letter from a future research experience would alleviate any such concerns even at most research-heavy schools.
Lastly, most decent people recognize that priorities and interests change, and that premeds will eventually leave the lab for one reason or another. From what you described, it does seem that you would benefit from amicably transitioning to other opportunities. Life is too short to be miserable when you've got other options. Just my thoughts.