I agree that this is annoying, but actually in my latest couple of games, I found that this is less of a nuisance if you deal with it in a different way than trying to take out all his apostles. In my latest game, instead I've done the following, which is much less of a nuisance (but possibly only works if you have more than one or two cities).
1) Launch an inquisition ASAP.
2) When his apostles come in waves, let them convert one of your cities. This usually takes quite a lot of charges if city is not small.
3) Once city is converted, sent in an Inquisitor and clear his religion, and let him start over.
4) Rinse and repeat.
Of course, this only works if you have enough cities for him to not convert all your cities in one sweep.
Another strategy that I find useful is the following:
1) Get an apostle with the bonus to theological combat promotion.
2) Park him next to a holy site close to your borders towards the following religion and put him to sleep.
3) Foreign apostles/missionaries will not attack him instead of converting your cities. If you just let him sleep, he'll heal between turns.
4) The foreign religious units will suicide themselves by attacking your units, thus giving -250 preasure of their religion and +250 presure of your religion within 10 tiles. Sometimes they wander off with low health, at which point you can snipe them with your apostle if you want to.
Of course, this only works if they don't send enough apostles to kill him in one turn, so you need to watch out for that.
