The Emperor *has* to lead the Catholic League, and until the Peace of Westphalia or a Protestant Victory, has to be Catholic.
Even when people start to pick sides, the Protestant electors won't vote for anyone who isn't Catholic, and should you join the Protestant League as a Catholic to get their votes, victory immediately makes you leader of the Catholic League.
So if you want Protestant Austria Emperor, best thing would be to try to fight the League War to a draw, and then convert after the Peace. This does depend on enough nations joining the Protestant side for them to feel brave enough to attack though. Depending on how large your actually holdings are, you might have to temporarily give up Emperor to become Protestant, and then hopefully tip the balance/get the chance to start the League War on the Protestant side.