If reports are to be believed in the papers that Rooney and his camp are denying that he requested a transfer suggests he wants to stay. The purpose of getting the club or Sir Alex to deny or he asked for a transfer is to try and avoid a negative reaction from the fans when he's back playing.
Here is what I personally think happened. Rooney was very annoyed at being dropped for the Madrid game and subsequently being played out of position and frequently also being substituted. That would have hurt his ego as well as made him insecure about his position at the club. Form aside, I can understand why he would feel that way.
So he had a informal meeting with SAF, aired his grievances as said something like "well if you're not going to play me propely, why should I stay at this club, I want to be playing all the time, and Im prepared to leave if thats what it takes". SAF would have been irked by such a response and probably let rip some hairdyer treatment. I imagine this happened just a few days before SAF announced his retirement plans.
However, as soon as SAF's retirement plans came out and mumblings of Rooney's discontent also emerged, so the media took over, the club and Rooney's representatives got involve, fans made emotional knee-jerk reactions and so positions became entrenched. One of SAFs final comments on this saga was he told Rooney to 'go away and have a think' ... ie initiate a cooling off period.
In this context, both parties are right: SAF is right that Rooney asked to leave the club (though not formally) and Rooney is right that he has not asked for a transfer. And is thats the case, a carefully thought out statement that allows both parties to keep face should be easily possible.
With a new manager, some new quality midfielders and perhaps even Ronaldo in the mix, I'd really hope we can find a way to keep Rooney, get him feeling loved and motivated and start afresh. I think a front three of Kagawa, RVP and Rooney under Moyes would be devastating, add Ronaldo to that, and we win the Champions League too.