I did not kill the Legion detachment in Nipton because they started walking away and I still had to search the town hall. So I went to where they were keeping the people they enslaved, and no one was aggro. I was allowed to walk up and free the slaves, standing right in front of their alleged guard. He totally let them walk away and kept ignoring me.

Side note, if you can kill off members of a faction with a silenced weapon while stealthed and out of sight of others, you don't lose reputation with them. If you're really good and can one-shot them (no small task with a varmint rifle) you can even do it in the general vicinity of others. I don't know if this is intended or not. So far I've killed those six Legion soldiers and a 3 man patrol, as well as the four ground level Khan members in Boulder City. I couldn't take out the three guys downstairs without being noticed but only got tagged for one or two of them, I'm now only shunned by the Khans and am still completely neutral to the Legion.

When I went in and freed the slaves, they all started shooting at me so... no clue what happened with your go.

I love this, I was killing NCR at the dam for their armor with the varmint rifle was quite fun.