If the doctor knows you well, it would not hurt to get a LOR from him. Your academic letters are most important but non-academic letters are common as supplements to your academic letters.
How it worked at my school was that at least 2 LORs were required from pre-req science professors. After that, I could get letters from humanities professors, volunteer work coordinators or doctors I shadowed (basically whomever I wanted). I managed to get 2 science letters and one each from the latter three mentioned. I thought this would help paint a diverse picture of me to an admissions committee.
Regarding whether to ask now or not - find out if your school's prehealth office or advisor will hold on to your LOR if you had it written now. This is how it worked at my school - I could have it sent to the prehealth office and they would hold on to it for up to 3 years. Ideally, you should ask for a letter when you feel the person writing it has had a chance to know you well and/or when an experience with the writer is ending and you are "freshest" in the writer's mind.
I would ask for an LOR, but maybe not until later. As the other person said, it is too likely that it can get lost between now and when you actually apply for medical schools. Having that LOR would definitely be a plus, as schools definitely like to see LORs outside of academia (the opposite of what some of the reserach-psychos around here will say... haha!)