The inches of difference in height between them do not make Bucky blink, the only thing that causes him hesitation is the knowledge that Thor is not supposed to be someone he fights but, at the same time, he is attempting to get in the way of the mission being completed. Thor is not his handler, he does not need to be obeyed, so he should not get in the way. The mission has to be completed.

He's half a second too slow to stop Tom getting kicked in the ribs, and that might be a little on purpose as he has no concern with seeing the man hurt, even if the Asset preferred a quick kill unless ordered otherwise (but he's not being ordered is he, he's doing this of his free will, spurred by vengeful and protective feelings of his own). That's all he allows though, as the moment after Thor's foot swings Bucky's metal hand grabs for the back of his shirt to throw him back against the wall.

"I said he's my mission." his voice takes on a low edge as he wheels to face Thor again, the plates on his metal arm shifting and resettling as he flexes it.

It would only take a second to finish Tom off if Thor would just let him do it.