However, Jones has praised Ledley's reaction to the decision and revealed the club are still hoping to negotiate a new contract with the £6million-rated midfielder.
He told the club's official website: "Joe understood the reasons why Mark took over. Of course he was disappointed but you can't have a skipper whose future is in doubt.
"The chairman is still trying to negotiate a new contract with him, will we cash in on him? We can only cash in on him if someone makes an offer, and nobody has made an offer.
"Once the transfer window closes we'll keep trying to negotiate with Joe. We will go to a tribunal if he leaves. I can't speak for the tribunal, but I'm confident we would get a good deal."