"If following these orders was a source of contention for the team than it could work for me. "

I could agree wityh at least some of the members of the team not always liking what they are asked to do. Mainly, this is a way to have them interact with the Marvel Universe as a whole. But the AF I am envisioning is more like the ones that originally showed up in X-Men, fighting heroes for control of Wolverine. Now, you have an AF that not only fights baddies, but heroes as well. This reminds me of the Avengers/Defenders wars of the 70s/80s. It used to be, that heroes did not always see eye to eye, so they fought. Much the same thing going on here.