Of course, the alternative to killing or deleting them is to just turn them into townies. I keep a small lot in a distant corner of every hood that only contains Inge's teleporter bush. Any sims I don't want to play (or new CAS townies I make) get put on that lot and turned into townies or downtownies. Keeps the character files from getting cluttered up with unnecessarily dead sims, and with notownieregen in place keeps the game from continuing to make its own fugly replacements for townies that do die, move in, whatever.
I do this with most of my "extra" spawn as well, since I don't care about time synchronization. That way I keep the genetics I want and can re-insert them as playables through move-in or marriage if desirable.
@ Deviancy: deleting the default neighbourhoods should not affect your ability to create custom 'hoods, except that, depending on what you delete, you might end up with a lack of default townies in your new 'hoods. This is a good thing, in my view. I generally leave the clean templates of the default 'hoods in, since I occasionally steal houses and lots (unoccupied, naturally) from the default 'hoods, if I'm too lazy to build, although I never play the defaults.