York confirmed last Saturday that they had added Stones to Adam Hinshelwood's squad after reportedly winning the race for the striker's signature.
He played in Oldham Athletic's competition earlier in the season and therefore missed the FA Trophy, where City were sent out 1-0 in a cup draw with Gainsborough Trinity.
Maloney admitted Yorke's interest was “completely out of the blue” and spoke about how the move came about, while Latics sporting director Gregor Rioch praised the Minsterman's conduct in the negotiations.
Mr Maloney admitted in an interview with Wigan Today: “The interest from Mr Yorke was completely out of the blue.”
“The plan was for him to go to Oldham and come back and play against Birmingham (last Saturday).
“I met him on Friday for the first time since he came back from Oldham and York made me a direct offer.
“We left it to Stonesea and it would have been really nice for him to come back and fight for a place.
“But he said he wanted to go to York, it’s a great opportunity for him and I wish him the best.
“But I think most of the money we get for Stonesea will go to make up for the losses we have.
“We might be able to use some of it, but we can't use a lot of it, and of course we can't afford it in terms of transfer fees. We can offer a lot more in terms of wages.”
Rioch added: “I have worked with Josh for a number of years and know how keen he is to play senior football on a regular basis.
“We have left it up to Josh to make decisions about his future path, but he has decided to make a fresh start at York, which we completely understand.
“We have been presented with a substantial offer that is consistent with our assessment of Josh and provides us with a good return, but it is a matter of protecting ourselves as a club if Josh continues to develop in the way we want. It also guarantees that.
“Firstly, I would like to thank Oldham Athletic for giving him the platform to show what he can do at that level.
“This presented an opportunity that was too good for Josh to turn down.
“York also acted with great professionalism to ensure the transaction went well for all parties. We wish Josh all the best in his future career.”
