Jones joined Cardiff in a swap deal involving Peter Odemwingie last week after a troubled final month at the Britannia Stadium.
The Trinidad and Tobago international was fined two weeks' wages by Stoke after making himself unavailable for the Barclays Premier League game against Liverpool on January 12.
Jones, who had fallen down the Potters pecking order, has insisted he was not on strike or trying to cause trouble, but making a stand to force a decision about his future.
Hughes said: "Kenwyne was frustrated because he wasn't playing. 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.
"He has moved on, we have moved on. I still felt he had a role here, but that wasn't to be. We made the move that was correct for Stoke City.
"Kenwyne is no longer a Stoke player, so I don't particularly need to speak about him.
"We wish him well but we'll try to get on with what we're trying to do.
"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."
Hughes, at a press conference to preview Saturday's game at Southampton, was responding to comments from Jones suggesting he did not regret his actions.
"The main reason was for my voice to be heard because they didn't want to pay attention to me," 29-year-old Jones, who struck on debut for Cardiff last weekend, was quoted as saying. "That's all I needed.
"I didn't want to disrupt the squad, disrespect the manager or anything."
Hughes feels his team have benefited from the part-exchange with Cardiff, with Odemwingie showing versatility by making his debut in a wide role in last weekend's defeat of Manchester United.
Odemwingie himself has had difficulties in the past, most notably his spectacular fall-out with West Brom last season.
But after the Nigerian failed to establish himself at Cardiff, Hughes is confident he can be a real asset for the Potters.
He said: "We are really pleased Peter is with us. He is a good guy and has integrated into the group quickly.
"He has got pace, intelligence and can take care of the football.
"He gives us something we didn't have and I think he is going to have a real effect on us."
Defender Marc Wilson could be doubtful for the game at Southampton after a chest infection while forwards Marko Arnautovic and Jonathan Walters are hoping to overcome knocks.