If you sneak around, use a silencer and never get into combat mode (Danger mark in sneak mode), you can get away with murder.
I managed to wipe out Cottonwood Cove while keeping Legion reputation on 'Neutral'.
That said, I would love to see the mod described in OP.
Do you have the latest patch? I run the game on Steam, so it is always up-to-date and it seems that this latest patch simply ruined this aspect.
You said that we can get away with murder, but not quite. Here, sometimes I achieve that,
most of the times I don't. I can't put my finger on it, I thought it was the companion but it is not; I just tried to kill an NCR soldier, there was absolutely no one around, and no matter how many times I loaded the game, I keep getting the "credits" for it (always using my silenced 22).
We urgently need a mod like Oblivion's "No psychic guards"...

Another thing: ok, I cand understand the requirement of a silenced gun, but and when there is no one around? Like inside a house in the middle of nowhere? I tested it with my trail carbine, got caught in the act by, I don't know, the spirits maybe.

This needs some serious tweaking, some serious fime-tuning... edit:
fine-tuning