The only way I see the master living through the fight in the cathedral is if before he died he used his psionic abilities to move his mind into a new body with that he escapes to plan and rebuild.

... And so the Master developed the multiple personalities. If you played all the way to the end of Fallout 1 and actually had a conversation with the Master (DEATH BY WORDS), you might remember that he would often talk in different voices.

Whose to say that the Master that you killed was the ACTUAL master and not just an extension of the master, who is comprised of both technical and organic material. Theoretically he could have absorbed a modem into a centaur and remote controlled the Master that you talked to.

They can do whatever they want through the magic of video games

Or just kill him and say a loony wrote the <3 master

Well, that's why we all love video games, right ? "Shit. Shit never changes."
Shit happens

well how about this. the enclave set up some sort of bulletin bored. pre internet style. the master could have uploaded himself to it and then maybe into a brain computer thingy similar to the one being the big bad guy in fallout tactics.

then again it could be just considered that when he was blown up his particles were blown up and the followers just "decided" that all living things breathed in his particles and are just acting as if he were GOD like/in all of us.

on that angle you would have to make them very much a cooky cult or the church in RL could get a little angry.