Obviously Sam is aware he crossed a line and hurt Bucky, but is he aware of just how deep the blow went? So I'd say yes, in the immediate sense: after all, he literally knocks Bucky off his feet. When Bucky starts begging Sam to punish him instead of Steve, his distress is apparent, and it's severe enough that Sam ignores his instinct not to touch Bucky (neither Sam nor Steve want to inflict themselves on him any further) and hugs him. But in the broader sense, no. He doesn't know how demolished Bucky already is: that he's not eating and barely sleeping, that he's afraid to leave his apartment, that it's only stubbornness and the need to protect Steve sustaining him through this conversation. More fundamentally, as the commenter below put it, he doesn't know that Bucky has lost his best friends and his main source of security and love. From Sam's perspective, he and Steve were abusers who frightened Bucky and subjected him to sex he hated. (Steve asked Bucky whether any part of their relationship was real, and Bucky begged not to be made to answer before arriving at, "People use me, or they don't." This was a terrible response, because it completely elided the very real comfort and affection. Similarly, when Sam asks what Bucky felt when they touched him, Bucky gives an incredibly damaging answer. It's understandable, I hope, because Bucky construes both questions as being specifically about sex. But he'd have done better to mention THE CUDDLES.) As Sam understands it, he thought he was in love with someone who, in turn, thought Sam occasionally hit him and tortured him sexually as punishment. Now that he thinks he knows the truth, Sam doesn't imagine for a moment that there was anything genuinely good for Bucky in that abusive relationship. When Bucky asks to go home, Sam has no trouble believing that Bucky just wants to escape.

Does he think Sam did it on purpose to punish him, or is he that devastated to think he made Sam and Steve feel as he felt after raping a target? Both. And Sam did lash out at him. Sometimes we say the wrong things because we don't fully understand the situation or where the other person is coming from, but sometimes (hopefully not often) we say the wrong things because we're upset and angry. Sam obviously didn't mean to hurt Bucky as badly as he did, but invoking Bucky's trauma like that was unkind and unfair. And yes, Bucky is appalled when he finally connects the things Sam and Steve have been saying to him (you made us into monsters, we never would have touched you, etc.) to the visceral horror and sense of violation he experienced when Hydra made him into that particular type of monster. He loves them and is devastated to think he's hurt them that badly (and he didn't, it is not the same, hence UNFAIR), and at the same time he has a sort of cognitive meltdown (triggering the worst and [spoilers] last of the headaches) because he is conditioned to be pleasing and yet somehow by following the dictates of that conditioning he has fucked up catastrophically.