The obvious solution to that would be to leave the religion that keeps declaring you a heretic. Basically, I think the protection against such an exploit works like this: you shouldn't lose H/P so fast that you don't have the time necessary to travel to a temple and leave the religion before it seriously hurts you.
No more than one H/P hit per week seems sufficient. If you go on a spree and send a bunch of heretical messages on a single day, you don't get one hit per message, you get one hit for the whole thing.
From a RP and gameplay perspective, I really like the idea.
Agreed, that's simple enough. Steady loss should be possible, not rapid. And if you can stab/capture/otherwise prevent someone from reaching a temple for a long time, while holding the Elders of a religion in a lock, then I think you deserve to destroy someone's reputation one nibble at a time.