Before Jones's exit, the Trinidad and Tobago international was fined two weeks' wages after refusing to make himself available for Stoke's 5-3 defeat to Liverpool on January 12.
"Kenwyne was frustrated because he wasn't playing," Hughes said in a press conference. "I said at the time I didn't think it was the correct way to go about it. He will say he was justified because he got a move and a longer contract.
"When you enter a [transfer] window, the key is at the end of it you want to be better than you were when you entered it. I think we are in better shape now than we were at the beginning."
The Potters are currently 11th in the Premier League table.