In my current game England has been excommunicated most of the time. This hasn't really been a problem, until the inquisitors showed up and started killing off my governors and generals. Is there any thing I can do about these inquisitors without resorting to assassination? How can I protect my loyal subjects from being burned at the stake?
If assassination is too chivalrous for you, I'd gladly suggest a much better, bolder alternative!
I understand your plight - the Pope is too risky a target for an assassination; risking a star agent and a good friend on the mission is a questionable decision. The inquisitors are annoying, and chasing them down is reactive behaviour; surely there is a better way.
Look at the Papacy. Now look at you. Now look at the Papacy again. Do you wish they were gone, daring to shout insults at you from what is (or will soon be) your own backyard? Make it so!
The Pope tends to keep his faction small; not that he isn't ambitious, rather his neighbors are about as capable as him when it comes to warfare. He probably only has a few regions; he may even be restricted to a single territory. Crush his annoying little state for offending you!
Sometimes, he may have the gall to call a crusade against you. This will rarely happen, and most of the time it will not even be possible - he is only capable of rallying Christendom every few decades, so more often than not, even if he wanted to, he would be unable to cause you more trouble than he's already started.
After ye've ripped off his head and spat down his neck, consider giving his successor a chance to repent for his sins and offer to reconcile with him - you are, after all, a forgiving soul. You're generous too: Give him back the city you took (sack beforehand, he won't care!), maybe even offer him a few of those you captured on the way (suddenly, the larger the Papacy used to be, the better!); don't forget to offer him an alliance so that you can protect him from those who seek to exploit his momentary weakness. More often than not, the new Pope will realize that you're the most faithful believer around, and your troubles will be resolved; if, at some point, he forgets who his best friend is, feel free to repeat the above - most Popes who would fall as far as to excommunicate the most pious nation around have lost God's protection, and you must do the Lord's work and reform the Papacy whenever necessary.
It's been a while, but I seem to recall inquisitors being pretty vulnerable to assassination...
Other than that, build many religious buildings to try and improve your piety.