Conscience and the Moral Argument as Evidence for the Goodness of God.

[The Architect Of Fate]

It sort of looks to me as if evolution hasn't made us all that peaceful.

It's made us peaceful not pacifistic. There is a difference  

Like maybe it's true that we want to be nice and friendly with the other 50-150 in our immediate group.

Considering humans have an adept ability to be able to integrate encountered groups into their own group (This is how nations form) this seems a lot more universal than you are letting on.

But then history shows that we have no trouble going over and massacring the 50-150 people in the next valley over, if we happen to want their resources. 

History shows a mix of intertribal mixing and integration and violence. And history shows that wars were rarely casual affairs and often had build-ups that were sometimes years in the making before getting to a full-blown slaughter. It's rarely a case of a bunch of humans waking up one day and deciding to just slaughter the tribe one valley over and take their stuff. 

Then if we're saying that humans are like other primates, don't some of those guys decide their leader through combat?

Note the word "some" and remember most modern primates have diverged from us significantly. Primate behavior is quite varied. 

 Like the alpha male becomes alpha by beating up the old alpha? And then the new alpha has sex rights over the girls? 

See above 

So there are a couple of things I think we'd want to resolve before adopting your view of things. 

So far you have not really brought up any. 

First, just because we evolved with a trait doesn't make it moral or ethical.

Why not if it's the reason why morals and ethics exist period 

 Maybe our reason and ethical sense says we should overcome traits we evolved with. We wouldn't want to slip into a naturalistic fallacy. 

Is it a naturalistic fallacy though? As he's not arguing its good because it's natural he's arguing the only reason there is any conception of good is that we evolved any concern for morality, to begin with, and without such a concept the word or idea of good is as meaningless as the term Wurplewoozle. Hell even if god were real and had put goodness in our hearts that would be meaningless without a care for it to begin with. 

Second, I see no reason to believe that evolution has made us peaceful. Or cooperative beyond a very limited scope.

 Well, the reason seems pretty clear it made us peaceful just not pacifistic were willing to use violence were just not totally sociopathic about it. 

It's admirable that you don't want to rape or murder anyone. But there sure has been a lot of rape and murder in history, which leads me to think that it remains a natural trait.

There is little evidence that it's a natural trait if it were natural why do militaries need to train men not just how to kill but make them want to kill someone they have never met and who has done them no harm? If rape were natural why do humans seem to have such a strong negative reaction to it? this can't merely be cultural indoctrination as even in cultures where there were few written rules in rape there seemed to be a disgust for the act.