As a member of a reserve (I know, it's not the same as active duty, but still) infantry unit up in New York, and having worked with guys from many active duty units, I'm confident enough to say that a vast majority of the US military would not be willing to fire on US citizens, so long as they're not fired upon first. Many of our servicemembers, especially those in the combat arms, own personal firearms themselves, and are just as concerned about their 2A rights as you are. The members of my unit, many of them NYPD in their civilian jobs, are furious with the new gun control laws passed in NY, and a good amount of them are refusing to register their firearms or enforce the law when it becomes active. Personally, I'm not too worried about the military getting involved in any confiscation scheme, and even if we were ordered to, you can bet that we'd half-a** it.
Just my 2 cents.