To travel hopefully is a better thing than to arrive

You know, I was worried at first that it was going to be Good Character Turns Evil, which I also dislike. (See: Garibaldi in S4. That storyline doesn't work for me at all because basically nothing he does is actually real, and that kind of programming/brainwashing/evil twin/whatever is almost always how that device plays out.) I thought the Machine had programmed him, or Walternate had done something to it somehow, whatever. But I think for all that Walter is talking about "weaponization," that was still Peter. Walter probably can't accept that Peter would do something like that, so he's looking for some outside influence, but until/unless I'm proven wrong later on, I don't think that's the case.

I mean, it was hard to watch him kill the shapeshifters, but from his perspective he thinks this is the best way to save his entire world, to keep him from getting caught up in Walternate's plan. Whether he's justifying it as an ends justify the means kind of thing, or whether he genuinely doesn't believe the shapeshifters are anything other than a weapon and that therefore there's no moral dilemma in destroying them, or both, I don't know that that necessarily makes him evil, or even more morally suspect. Like you said, he was a con-man for a long time. This is probably more in tune with who he actually is than anything else.