Avengers can have a nasty habit of shooting first and asking questions later.
So, if you're going to allow Avengers, you have a few options there.
A) Make it so that the Avenger will be forced to work with the supers via...well,
force if nessicary.
Pro: It lets you run your story, while still allowing avengers.
Cons: A player who has it in his head that his avenger ain't gonna take no
crap from no fucking rot will find himself not having fun, as every time he tries
to do what he feels is his character concept, he's forced to not do so. This can
lead to a bitter player.
Allow Avengers only if the player understands from the get go that he will
be forced to work with supernaturals.
Pros: This, also, lets you run the story, while still allowing avengers.
Cons: It limits on certain aspects of the Vengence creed, and also limits
certain concepts. It might also force players to make an avenger that's slightly
less powerful (if you demand that they have vision or mercy dots).
C) Simply do'nt allow avengers.
Pro: This will definatly allow you to run the story the way you have envisioned
it, without worrying about stepping on player's toes in game.
Cons: It completely eliminates one creed from the game, and all possible role
playing things that would stem from it. It also really limits certain concepts, and
it also might not even ssolve the problem (I've seen some people get it in their
heads that Defenders are just like Avengers but with diffrent powers).
There you have it. The pros and cons of your most obvious options. That
said..I think the idea is really neat, and has some pretty good merit.I wouldn't
mind playing in just such a story myself.