No, I would have expected you to flag. The problem the assistant had is that he obviously knew Rooney was in an offside position, but he would not have known how close the ball went to Rooney. So the flag should have gone up and the referee would then have to decide if Rooney was interfering with play. He was interfering with play as he had to move his body so that the ball did not touch him, and he was also interfering with an opponent as he was clearly in the eyeline of the goalkeeper. I would say that the goal should have been disallowed.