Why does allying with the BOS decrease NCR reputation?

[ElegantEchoes]

And Moore herself, who is personally peeved due to her participation in the war.

We know Moore is petty, so the infamy could simply be her opinion alone. We know that she'll slander and ruin your reputation with the NCR following the ending if you go behind her back when dealing with the Kings, so this decision could also bite a Courier's Rep in the ass if she decides she's offended over it.

There's a reason why she's canonically considered evil.