In which we watch Avengers multiple times.
Barton’s post-brainwashing guilt is a quite reasonable thing the first time around. He just rounded up a bunch of his enemies, blew the shit out of his own headquarters, and killed a bunch of friendly soldiers and guards. The second time around—again, humor me, there is a lot going on in this movie—it comes across a little more strongly.
I mean, it’s not really a “Do as I say” sort of brainwashing. It’s not even a “Follow my orders really enthusiastically" sort of brainwashing. Check out the random suit that Loki zaps along with Hawkeye and Selvig before the bunker blows up. They’re hustling out, and Duder McGee puts his hand on the small of Loki’s back. It’s not a random gesture. He’s in bodyguard mode. (Rogers does almost the exact same thing to Stark after the helicarrier attack begins, before Stark gets back to his armor.)
The next time we see them, Hawkeye’s giving Loki a shopping list comprised of “a distraction and an eyeball.” I mean, yes, brainwashed, but Hawkeye basically put a hit on the guy Loki kills in Germany. And dispatched Loki to accomplish it. Honestly, Brainwashed Hawkeye is responsible for a phenomenal amount of carnage. Loki doesn’t know shit about SHIELD’s enemies. Guess who’s got them all on speed-dial all of the sudden? Loki doesn’t know shit about SHIELD’s secret bases. Guess who’s arrowing their guards in the face and breaking into their vaults? Loki doesn’t know shit about how to blow up SHIELD’s helicarrier from inside it. Enter Hawkeye, stage left, adjusting for windspeed and firewalls. The Tesseract’s conversion message is “Want to fuck shit up just as badly as Loki does, independently come up with and execute your own plan to fuck shit up in such fashion, remember—the goal is to fuck shit up.”
So basically Hawkeye winds up with a lot of stuff that, while he isn’t strictly on the hook for, he’s going to feel like he’s got on his conscience. (I think this is how Black Widow winds up being The Fun One whenever they go places and do things. Like, okay, she maybe burned down a few hospitals or whatever, but she doesn’t feel so guilty about it.)