I don't really care about Karma at all, a lot less than F3. What I care about is losing reputation with them, will that happen if I do an undetected stealth kill?
The Colonel meant reputation it was a misplaced word.
Second any silent undetected kill will not lose reputation with a faction.
Try any gun with a silencer, or a melee weapon that is not powered like a chainsaw, thrown weapon or any unarmed weapon.
Long range kills even without a silencer are the same, but 1 are more likely to be detected ( automatically with certain companions in party ), resulting in rep loss.
And 2 will most likely turn any friends of the npc hostile, in fact I would say always turn them hostile.
If so leave and return later on.