Bear in mind that said HYDRA terrorist was quite literally brainwashed and turned into a living weapon against his will. Bucky Barnes would not have knowingly, willingly signed up with HYDRA; those guys pretty much kidnapped him from where he fell to his presumed death in The First Avenger, brainwashed him into a barely conscious weapon, and kept him on ice for 70 years whenever they didn't need him to do some killing for them. He's as much a victim as anyone and everyone HYDRA sent him to kill, but of course, only Steve and those closest to him, plus the audience, actually know that, so from an in-universe standpoint, your point about Steve harboring a fugitive from justice and sheltering a terrorist is perfectly reasonable.
He did get assaulted, from what I remember of Age of Ultron. Steve tried to sock him at least once, probably that fight scene when he thought that Tony hadn't learned his damned lesson and was at it again trying to make a new artificial intelligence to fight Ultron. And Thor did kind of choke Tony out after Ultron first unveiled himself. So in terms of exact words, Tony did get jumped over the whole Ultron situation.