Clint didn't expect her to attack him. He was knocked out once she hit him on the head. The was enough for Loki's control over him. He was unconnious and breathing heavily. LOki meanwhile was asleep and didn't know what was going on.
Barton awoke and was looking around. He groaned holding his head. He realized what he had been about to do and he felt guilty. He cared about Natasha and he didn't want to hurt or kill her.
He saw that she was wounded. He knew it was his fault.

Quickly as he could he unchained her and carried her out of the buillding. He was a bit dazed and confused. But he had to focus on getting her medical help. She was still unconnious when he did. He just hoped she didn't wake till he got her there.
The man knew she would be mad.
Clint stayed outside the room letting the medics tend to her. He had been very close to killing her and it made him feel sick.