***SPOILERS, BUT I NEED HELP*** 
I was on that quest where you go to check out Nipton, and it turned out that some Vulpes dude with a wolf hat had rounded up the whole town and brutally butchered them. Anyways, I'm playing a sort of good character, but I tend to be very brutal. He told me what he did, and I killed everyone there, included Vulpes. (really liking my new wolf hat :) If Caesar and his people aren't really the "good" guys around New Vegas, then whatever  I did the right thing. However, do you guys think I should reload the save right before I killed him, and let him go free so that I can get in close with Caesar? I don't plan on doing any sort of evil stuff, so associating my character with him might be a bad idea. Was killing Vulpes a bad idea, or the "right" thing to do?

I don't think it'll prevent you playing however you want to play later in the game.  At a certain point Caesar and the NCR offer you an amnesty for any previous crimes against them.

Later in the game you'll be given a pardon from Caesar for any crimes you've committed against the Legion.  This is part of the main quest, so you shouldn't worry about it.

I let them go but eventually made my way to Caesar's camp and butchered them all, (not quest related, just how I roll) 
 
If you are playing a good character through and through I would say stick with your path, the only reason I didn't kill him was that I could make a hard save further in so I could reload it to see the Legion's quest line if I ever decided too. 
 
And actually I don't know if killing them like you did really matters, once you get to vegas and see Mr.House and talk to Benny, the NCR and Legion give you a pardon on all your past crimes so their leaders can talk to you.  The only thing I am wondering is it is Vulpes who comes to give you the pardon, so I guess it would be another NPC that takes his place?

  The only thing I am wondering is it is Vulpes who comes to give you the pardon, so I guess it would be another NPC that takes his place? "

Yes, another character show up.  He mentions you killing  Vulpes.

When I got there, I totally tried doing the same thing, but got absolutely massacred by them, so I opted to just let them leave. 
 
But my actions sense then have gotten The Legion to vilify me, so whatever. Those guys are assholes. 

There are no "good guys" really, maybe the Followers. Unless you support Ceaser, you will eventually fight his men.

I wouldn't worry about it. I just went back on my latest playthrough with Boone and cleared the place for exp!

" There are no "good guys" really, maybe the Followers. Unless you support Ceaser, you will eventually fight his men. "

I don't know, I would say the side that pillages smaller tribes rapes their women and turns them into slaves would be the bad side…but that's just me... 

There's no true  "good faction" in the game, I'd just say the Legion is the worst of them all considering how far they take their crimes. Besides it means you can feel really great about slaughtering them en masse. 
 
I ended up taking out Caesar's (including the man himself) entire camp about 2/3 into the game and had no problems finishing it aside from some terrible crashes that plague the game anyway.  Granted I sided with the NCR.