The 29-year-old joined fellow Premier League strugglers Cardiff in a swap deal involving Peter Odemwingie last week.
Shortly before his transfer, Jones was fined two weeks' wages by Stoke after making himself unavailable for the league game against Liverpool on 12 January.
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 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."