Okay, small update on what has been happening with my attempts at karma modding. Just to have these observations in writing, so that other modders might see them if they ever decide to try their hand at modding this feature as well.
First of all, it is, naturally, not nearly as simple as simply changing the karma loss/gain for enemies of different karma.
New Vegas and F3 are both extremely inconsistent and chaotic with karma allocation. NPCs are mix and match of different alignments, and there is a feeling that a with a lot of the npcs the devs simply didn't bother. Same thing with creatures, to a ridiculous degree, with Ant Queens and dogs being neutral and ghouls and roaches being evil. Try to mod bad karma for killing npcs - you'll get the same changes for ghouls, for example.
The solutions that I know of, are to either manually and tediously allocate karma values to each and every NPC and Creature, to have them rigidly in categories, or do the same with scripting.
[collapsed title=Some script commands for myself for later] http://geck.bethsoft.com/index.php?title=SetBaseKarma
http://www.gribbleshnibit.com/projects/NVSEDocs/#ListGetCount
http://www.gribbleshnibit.com/projects/NVSEDocs/#ListGetNthForm
SetGameSetting[/collapsed]