You can break your vassalage with the Pope if you're the emperor and he will still remain in the empire, be unable to attack you, and be integrated when you pass the last reform and become the HRE. The only downside is that he gets an 'overlord abandoned us' opinion modifier that can hurt your PI for a few years.
But yes, I agree that the Emperor should not be punished for the subjugation of the Papacy if the Pope voted to become a vassal of the Emperor. And the reformed Holy Roman Empire shouldn't get the 'Give Rome away' event either.
Oh, and while you're fixing that, PLEASE let me keep my Personal Unions in the Empire when I revoke. Especially if they're electors. I already have Grand Duchy and its stupid that my loyal inheritable Bohemian Union Partner magically becomes a vassal when I make the rest of the HRE my direct subject. The Habsburg Emperors would never have given Bohemia up like that.
