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The LOR is a snapshot of who you were at the time the letter was written, not a binding contract. The "transaction" has already been made at the time the letter was written as a result of your previous actions, so you don't owe them anything *more*. So don't feel guilty for leaving.

I guess my primary concern would be: If you don't get accepted this year, will you feel comfortable asking this person for an updated letter next year? Have you continued to produce the same high-quality work on the job in the few months after receiving the LOR?

I've been an even more sticky situation before — I announced I was leaving, *then* I requested an LOR for a job app, *then* I left the job a few months later. And later that year I asked for *a second* LOR for my med school app. Obviously this whole series of events was quite delicate to execute and could have been planned out better. But I think it was received well because I left on good terms with everyone, followed through on several projects in my last few months on the job, and was respectful. I agree you don't want to leave *immediately* (say, within 1 month) after getting the LOR, just for professionalism's sake. But as long as you continue to produce the same high-quality work, my gut feeling says you should be fine leaving.

(Whether or not this is a *good* LOR is another question, since you mention working with many docs who may or may not see you every month. Have you considered asking your manager for a LOR?)
 
If your manager is another med student it doesn't really make sense to ask them for a letter. They're more like a peer than someone who can give a meaningful evaluation at the level the ADCOMS want.

The physician letter will have to do. Maybe if you still have the chance, you might take several paragraphs and highlight specific qualities or anecdotes you would like the physician to comment on so that there is more substance.

Maybe other folks here will have differing suggestions for you as well.