When your wife is the acting police chief, who is going to arrest him? Who is going to file charges? Especially when it's the same guy that killed the former police chief of the town (and 2 FBI agents).
And who is to say he was defenseless? Maybe he had a gun on him. If you have reason to believe someone is armed and dangerous, well...
While it's not even remotely in modern times, one example I can think of is Jesse James. He was shot in the back. No breaking and entering, but he was screwing around with a picture on the wall and a supposed friend of his just pulled out a gun and shot him. And previous to that, Pinkertons once threw a bomb into his mother's house (which didn't kill anyone, but I think took someone's arm off).
I think also Gus had to do it himself to redeem himself in his own eyes. Letting him go (because he was afraid of him) was eating him up, then shooting his eventual wife by accident was even worse. He had to do it.