Peter may be a very clever wizard (more so than people give him credit for, I think), but ultimately he has little honor in him. I think he might have made a better Slytherin based on what we've seen of him so far - but I also thinkt that the Sorting Hat is never wrong, and that Peter will prove that he's a Gryffindor by some incredible act of bravery and defiance yet.

Betraying the Order wasn't brave and defiant?

I'm afraid the Hat doesn't say anything about Gryffindors being honorable. Even with JKR's bias, it's still demonstrated that in every house, there are people who behave honorably and people who don't.