This is the very first time I've done this quest. My character, being of good alignment, is in two minds about completing this quest, seeing that he was tasked by a Daedra an' all, especially seeing that the priest who I'm supposed to kill seems to have rebelled against his former master, which seems like a good thing. They also seem more like victims of the Daedra than true evil characters. But then again all of the Afflicted seem incredibly hostile and attack on sight, which isn't exactly the act of good aligned characters. They're also there supposedly preparing some sort of mass bio attack on Tamriel. And I understand that if I do destroy their home we start to see them out in the world attacking innocent people! So what is the best thing to do, leave the seemingly ticking time bomb or what looks like akin stirring up the hornets' nest by destroying most of them? What's the best thing to do on a RPG level for a good character?

Also, something strange has happened. My weapon was gathering souls like a pro right up until I entered Bthardamz, at which point it seemed to stop. I restarted from outside via a save I made. Yet again it seemed to stop collecting souls as soon as I enetered the ruin. Anyone know what could've caused this? And yep, it's fully charged and I have plenty of empty black soul gems.

Doesn't matter, they will attack you in random encounters.