Ok, here's my 2 cents worth.

1) When the guy with the strange hat appears, your general/agent RUNS. No excuses. If you walk up to him and he burns you, I think you're just asking for it.

2) The more guys these papal agents from hell burns, the more deadly they become. Their retinue of executioner + hunter of heretics trait line will make them living saints in no time.

3) As other fellows have mentioned, you can use the "surround with military units" method to kill him.

4) There's an incorrect component in the traits file which makes your generals spawn with 0 piety. All generals should start with 3 initially. Hope that buys you some protection.