Just offhand from my sci-fi experience, the gap between medical and military nanotechnology would likely be delivery. Medical kits can be directly applied to the areas needing treatment, allowing the nanobots or whatever nano-analogue you choose to reach their objective with minimal energy expenditure, environmental exposure, and lifetime. A weaponized version of this technology entails number of other considerations, such as protection of the nano munition in transit, as well as arming and dispersion mechanisms.
(In fact, if it is to be integrated into the technology tree, it may well follow the Plasma weapon research paths, as this line of alien weapons seems to overcome similar hurdles with their handling of projectile plasma.)
Personally, though, I'm a bit more in favor of pseudo-nanobots, as barely-visible (to the naked eye) machines programmed to assist/automate open-wound repair and patching, possibly even capable of assembling into temporary surgical tools, such as staples, pins, stitches, etc. Combined with some biological and chemical treatments, they could plausibly offer quick battlefield patching, while still maintaining the storyline importance of hospitals.
