Peter chose to go back with Walternate. I can't blame him. He didn't know that September told Walter that he could never go back, that the consequences would be disastrous, but Peter wouldn't have listened once he figured out he'd been lied to all of his life. So Walter holds as much blame as Peter does for his choosing to go back. Of course, hindsight is 20/20, and he should have told Peter where he came from, why he was here and why he couldn't go back once he would have been old enough to understand. Then again, we always watch these things as if they're really happening and we always have our own ideas about what should have happened, not thinking about who's writing it and what their vision of it all is. Everything is all written out and scripted and there's nothing we can do about it except lament over how we could have done such and such better or how so-and-so is so wrong for what he did. Even the actors don't have as much control over their characters as they'd probably like to have and Joshua Jackson is no exception. I don't know how he feels about how Peter was written in the past, but I do know that he's at least the tiniest bit perturbed that the writers have written it so that Peter has been fooled by Red for a lot longer than he should have been and I've been saying that for a long time myself.
My feelings on the subject: both Walter and Peter were dumbed-down so that Red could remain undiscovered for longer and nothing anyone can say to me will convince me otherwise. Actually, several people agree with me, or haven't disputed it, when I said as much in review threads on the episodes at Ex Isle, a BBS that I frequent and am a Supermod at-Supermod being a moderator who can moderate any forum on the board, but who doesn't have administrative privileges. I can do anything the moderators can do, but the moderators are restricted to their assigned forums.
Why do I think that the two geniuses have been dumbed-down? Well, both of them have known Olivia for two years at the very least. Walter knows Olivia's moods without her ever having to say anything and Peter was falling in love with her through both years-yes, it was very subtle, and I still saw it, and I liked it. Peter, upon first meeting and speaking with Red, commented that her eyes were a different shade than Olivia's-one had darker eyes than the other, I can't remember which-then he didn't notice it once the switch was made? I've heard that love is blind, but we're talking about two geniuses here, who are two very observant men to boot, and neither of them, when they notice that the Olivia who is with them is different from the one that they've known for two years, think or say anything about it? Well, I admit that Peter did say something to Red about how different she was, but seemed to accept her (rather weak) explanation that crossing over had changed her. He never seemed to question it again-even when she got Casablanca wrong by asking if it was Ronald Reagan who starred in it. That should have been a trigger right there that she was from the other side, but no, he had to get a call from a cleaning lady in NY giving him Olivia's message before the light bulb went off and he's thinking "Oh shit, I'm f---ing the wrong Olivia!"
I know that was a crude way to put that, but it's no less true. I could pretty it up and instead say that he's thinking "Uh oh, I'm sleeping with the enemy!" but I'll stick with my first thought because that's what she's doing, she got desperate after he told her that how different he found her, and thus threw herself at him. She's supposed to have a fiance-at least that's what Wiki said that Frank is, he's at least her boyfriend, yet she had no trouble dragging Peter into her bed to protect her identity. I wonder how Frank will feel about that, or if she'll even tell him. Personally, I don't think having her throw herself at Peter like a cat in heat was necessary and since she did, I'm going to fault him again for not seeing that his Olivia would not have done that. Sure, she kissed him when she went to get him, but not like Red did when she threw herself at him. Olivia's kiss was full of emotion and Red's was nothing more than calculated to evoke the reaction that it did-namely get him horny and distracted and forget that he was becoming suspicious of her.
Oh well, writers often contradict themselves to make a story go the way they want it to go, I guess Fringe is no different.