Let me explain:
Karma wise FO3 is very black and white...
This one is either very cynical (which doesn't fit any other documented quest) or just badly written.
In detail:
If I were to use the most peaceful option (all speech checks) The real bigots are the only humans to survive (they'll leave on their own accord). Every other single occupant will be slaughtered..
If one talks to Roy Philips he is shown to be as much, if not more so a [censored] than the tenpenny residents.
Even after finding out what Philips did... they see it as a minor mishap.. even threedog laughs about it.. WTF...
What is worse... He is still regarded as someone with good karma.. WTF #2
Now the bad option.. I can understand the true evil side of this quest (as Gingy explained.. killing TP residents yourself or let the ferals do the job), however the job itself.. ... is the game telling us that ghouls are better than people...? WTF #3
If I go back to my first PT... this quest actually made me angry, apart from the karma reasons..
If I do the "bad thing" I get caps...
If I do the good thing... I basically will activate a "cheat" which make me able to traverse dangerous grounds with ease. (after BS it became a blessing because you could avoid reavers.. *&%$##$!)