I suggest you PM KP2001. He's a Naval Flight Surgeon and has the best info on MD accession programs in the Navy.
I can only speak to USNA opportunities. Up to 24 mids per year may apply to attend med school right after USNA. Your major isn't critical, BUT you must take the courses required for med school admission. The toughie is Organic, which is a 3-6-5 course and a killer with the heavy load all mids bear. Thus, most med school aspirants major in Chem or Oceanography, as both majors require Organic and thus you don't need to find a way to fit an "extra" 9 hours for two semesters. Or, you can go to summer school each year to pick up any needed "extra" courses.
If you want to go to med school, you apply to the school and apply to USNA/the USN to let you go. You can go USUHS (free but incurs longer obligation) or a civilian school (I THINK USN pays tuition and a stipend and you pay room/board, etc.). I think that you have the choice b/t USUHS and a civilian school but that the USN gets to select which civilian school you can choose. I.e., you get into med school at Harvard, UVA, UTexas, and USUHS, the USN will choose among the 3 civilian schools and give you that choice or USUHS. That's the way it used to be -- things may have changed.
Note that the Navy has to allow you to go to med school. Generally, if they think you are likely to be accepted, they will let you go forward with your application. However, remember that the med school program, as well as the number of mids who can participate each year, can be revoked/modified at any time.
Finally, USNA no longer "discourages" candidates from saying they want to go to med school after USNA. Instead, they want to ensure that candidates are open to other service selection options in case that, for some reason, med school ceases to be an option.
