Other than wallowing in ignorant self-righteousness, your playthrough will be just fine. Claiming to have the moral high ground over the Legion and then killing them for it is just another form of barbarism.
At least I'm not crucifying them and putting their heads on sticks.
Status update, I found more crucified bodies at Cottonwood Cove. After I wiped out the encampment, of course. Boone seems to have a really good time with it. I took the boat out to the Fort, and wiped out the few Legionnaire's before the main encampment. I have a feeling I'm in for a fight when I go in there.
And to the person who mentioned doing the bidding of the NCR, I do not believe I am doing so. I would have been doing this regardless of their feelings. I still have not joined a faction, and if I can have my way, I will not join any at all. I'm just not sure if that's possible or not yet because I haven't gone that far in to that portion of the game as of yet.