Originally Posted by Hyde
For once, I actually agree with you. To me there's just too much suggesting Hawkeye won't be an Agent of SHIELD come Age of Ultron. First there's the fact he killed friends and co-workers and nearly took down the Helicarrier which is bad enough on it's own.
Second is he's the odd one out in the roster. The other five have/are all making appearances somewhere in Phase II, even Banner who doesn't have a movie. There's a chance he could cameo in Winter Soldier, but so far we've heard nothing on the Hawkeye front except for his big role in Age of Ultron.
Third, if the rumours and common fan beliefs are true then by the end of Cap 2 our heroes won't be a part of SHIELD anymore and would have gone underground. Hawkeye's friends/comrades/fellow Avengers. Would he stay with an organisation if they were hunting his friends, who he believes to be in the right?
Finally, as stated in my first point he had a God inside his head and forcing him to kill friends and endanger thousands more. That's going to psychologically **** him up. Would he still want to work for SHIELD after that? If I was him, I'd definitely take some time off or leave completely to think things through.
And I'd be right in saying that Hawkeye wasn't always a SHIELD agent in the comics, right? Was he at all in 616?
Personally, for reasons already stated, I think SHIELD would pardon him for the crimes committed by Loki's supernaturally induced command.
But I agree that it would make sense for him to want to take leave after such a thing. If Selvig is messed up due to being exposed to things the human mind isn't ready for, then Barton would be messed up from guilt and maybe also need a sort of soul searching to reaffirm his own independence (being that it was so violently ripped from him).
So I could see him just taking it easy at the beginning of AOU, with maybe a limited correspondence with SHIELD which allows him to hook back up when the team needs him, if they don't seek him out first.