Why did it have to be Clint Barton at all? There are other characters that are much more willing to use lethal force and it's not like Clint had even been in the story for more than a few panels at that point so it did come out of nowhere.
If Bendis felt that it just had to be Hawkeye for the shock factor of a good upstanding hero not known to be okay with lethal force then I think he should have had the courage of his convictions to make him Banner's killer without a cop out for fans to argue that he's not really a murderer. There are ways to make him more sympathetic, maybe in the vision we see that someone Clint cares about is killed by The Hulk or that while everyone seemed to be dead he particularly died in gruesome circumstances which affected his thinking when he and the others went to confront Banner.
I don't know if that was Bendis' intentions when he started but it definitely benefited from the Hydra-Cap story brewing the background of other books. What I found kinda cool is his actions in the main book could easily be read as real Steve is you unaware of the Hydra-Cap story his actions and words work very well as classic Captain America but if you are aware of Stevil and the whole Hydra-Cap story line everything he does comes across as deliciously manipulative.