Given that modifying an RNA virus to obtain specific results from an infection is very hard to begin with, also working with the limitation that your changes to

Given that modifying an RNA virus to obtain specific results from an infection is very hard to begin with, also working with the limitation that your changes to the virus have to look "natural" makes it essentially impossible by being impractical. On top of that, there's no reason to do it for a military weapon. For military use you don't infect a few people and hope it spreads, you infect a whole bunch and hope the whole thing spreads quickly enough that the virus can't be stopped, and it overwhelms an entire population by incapacitating or killing them. Dispersing virus over a significant fraction of a population isn't easy or quiet, so whether it's a natural disease or GMO doesn't matter, because they'll know who did it. The only scenario in which it makes sense to evolve a genetically engineered weapon in a way that hides its origins is for bioterrorism... and bioterrorism is very rare because it's a lot harder technically than terrorism that consists of shooting up a military base or running an exploding motorboat into a ship.