Stoner was showing Honda what he is capable of by not letting The Doctor finish third.
He proved he was capable of stuffing a 7 time champion with a broken leg that hadn't raced in 6 weeks on hte inside in the final corner. If Rossi was 100%, I think he would have been fighting with Pedrosa for the win.
Actually, he did manage to outsmart Rossi on that last set of turns. Rossi blocked him inside on the 1st to last corner so Stoner read that and changed his line for a better drive out of that turn and into the final corner. Stoner just barely made that pass stick. Actually he had to push Rossi off liine to make it stick. Clean racing, but very, very aggressive. If he had crashed on that move and taken Rossi out... Stoner wouldn't have made it out of the paddock alive without armed guards.