Playing Fallout as a goodie character, pretty good talking skills.

So I'm in Necropolis, I've killed the mutants (quest by Set, the leader of ghouls), fixed the waterpump (quest by the peaceful ghouls in the sewers) and got the waterchip from Vault 12.

I go to see Set the last time and his minion gives me some small reward for killing the mutants, and then Set seems to want me to leave, but he will still reply to my questions.

However, two walkthroughs I've seen seem to suggest to kill Set. One of them killing him and his minion ghouls right away. even before talking to Set and receiving the "kill the mutants" quest from him, while the other walkthrough claimed that after you have killed the mutants and go to talk with Set, he will attack you anyway when you ask for some more questions.

Well, that didn't happen to me. Set seemed relatively content, as long as I didn't talk aggressively or negatively to him. So, should I kill him and the other ghouls in the cathedral anyway? Is there any benefit to that, other than getting the experience points from killing more ghouls?

It just feels "wrong" for me to deliberately pick a fight with him since he seems cool with me, but is he an evil person that should be killed anyway? Does it somehow help the peaceful ghouls in the sewers (for which you fixed the water pump)?

Similarly, I didn't kill Set, because I didn't have a reason to. He's not exceptionally nice and you can be in a situation where he'll attack you, but if you do what he asks there's no reason to fight him. I don't remember anyone giving a quest, or reward for killing him, so you'll just get some exp. and items.

There's no "detect evil", so there's no answer whether he is and therefore should be killed. It's your choice, it may influence the ending of the Necropolis, though.

Do you remember in your ending, what happened to Necropolis?

I presume I got a good ending for them, something about the ghouls learning to live by themselves and coming up with some sort of business that they could sell to other factions. So a live-happily-ever-after for Necropolis, as far as I could tell.

I am just wondering if it affects e.g. the ending for Necropolis, if you leave Set alive (as it did seem he was a bit of a despotic leader and the peaceful ghouls in the sewers didn't like him)? I killed him and got the that ending for Necropolis.

I always take too long to get to the Necropolis. Everyone is always dead by the time I get there :P

I remember that this part was really tricky if you wish to have "good ending" for Necropolis - I've played in this game years ago, but as far as I remember, helping Set is leading to open conflict of ghouls with mutants and in effect - oblivion for all Necropolis "citizens". Well, in fact even if didn't help Set and get rid of the mutants it was still effecting in invasion on Necropolis. Of course there is also case with fixing the pump, but that was probably the easiest part. I'm not sure if I'm correct, but I believe that killing Set, reparing pump and some weird way to get rid of the mutants were required to have good ending for Necropolis (two things were required - eliminating the threat of mutant invasion and reparing water pump). The last condition was always unclear for me though. It was bit annoying, because I didn't want to use some walkthrough, and having good ending for other locations way less difficult to figure out.

When I played my party came up the manhole inside Set's building. I opened an ice locker and some ghoul thought I was stealing his dinner, so all hell broke loose. Never got a chance to talk to Set or the other named ghoul...
So you can always provoke the ghouls into attacking you.