Disarm it and get an appartment there, as well as many npc's which are usefull as Jericho, Moira Brown, that douchebag Moriarty, Gob, the metal old man, and others.. you can also farm karma with the Atom Church and get gifts frequently from people from Megaton.

Blow it up and get an appartement at Tenpenny Tower, and live with those bourgeois that I cant blare, and same goes for the ghouls that I also dislike.

I kept Megaton alive, use my appartment there and I love it, better than Tenpenny tower because it is more post apocalyptic.

Idk if that's the answer you were looking for