My guess is that the criteria for an excellent physician LOR contains:
1) Personal observation of you working with patients and treating them well.
2) A belief that you fully understand the hardships, commitment, sacrifices you will make when entering medicine.
3) A belief that you can handle the rigors of medical school.
4) For DO's, an understanding and belief in the osteopathic philosophy of medicine.
That being said, if you cannot get a DO LOR, then certainly you should go with the MD letter. That letter would be best if it either specifically mentions the above things, or by some other analogy, endorse your application to med school.
In your particular case, since your interaction with the MD is through research, perhaps emphasizing dedication to the research project, attention to detail, working long hours to make sure the job's done right, will be apt analogies. Scrupulous honestly in the reported data. Working well in a team. Perhaps even a demonstration of your knowledge of how your research will fit into the 'big picture' of heath care, medicine, or science in general.
- Tae