Why do you think Petyr helped Ned figure out Joffrey is a bastard if he was just going to betray Ned anyway?

In order to put the Starks and Lannisters in conflict. Petyr wants a prolonged civil war to allow him to rise in power and then turn on the weakened participants. That requires Ned to move against the Lannisters so that the Lannisters will move against him and then the North will retaliate.