Basically, he's decided that he can't continue to be both Neal's handler and friend, so given the choice he's choosing to continue to be Neal's friend over being his handler. Which is a decision I would've thought a lot more of the fandom would be all over, honestly -- in a way it's the ultimate acknowledgement of the thing the show has spent the last few years building up to, that when it comes right down to it Peter is irrevocably and utterly emotionally compromised by Neal; there's no sorting things into "professional" and "personal" boxes anymore. And he openly acknowledged that he thinks of Neal as family; I think this is the first time that he's come right out and said it. And I think the way he says goodbye at the end makes it obvious that he doesn't want things to change too much; Neal might be taking this as a final goodbye, because Neal likes big gestures and isn't so much for emotional in-betweens, but Peter isn't.
(Now whether Peter's "solution" is a good idea, or will actually work, is a different story; Neal's amply proven in the past that setting firmer boundaries just results in Neal finding creative new ways to break those boundaries. I doubt if Peter is going to hand Neal over to someone terribly hardassed -- there's no way Peter wouldn't vet any new handler six ways from Sunday, and his poor replacement handler is probably going to get Peter looking over his shoulder constantly. *g* I do think some space is good right now for all three of them -- Neal, Peter and El -- but I suspect they'll be terrible at actually maintaining it ...)
I think the thing about the rift between them this season that breaks my heart is that they're both trying so hard to do the right thing: Neal making a deal with the devil to do what he feels is best for Peter, and Peter ripping his own heart out to do what he thinks is best for Neal. I can understand Neal feeling rejected and hurt right now, but I can't imagine him being so petty as to hold a grudge long-term -- last season Peter forgave Neal easily for beating him up and throwing him out of his life; Peter pushing Neal away this time is far gentler and more loving than Neal's rejection in 4x09. I mean, like I said, I can understand Neal being hurt and upset about it (in both cases, actually; it's not like I hate Neal for rejecting Peter in 4x09, either), but if Peter backing off a bit is truly an unforgivable offense in Neal's eyes ... then Peter really has been throwing his friendship down a black hole all this time. But I don't believe so.
Like I was saying to
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... basically, I guess, I think this is painful for them in the short term but in the long term it's a good step towards both of them eventually being able to approach each other somewhat more as equals rather than boss/subordinate or mentor/mentee, and towards Peter getting a better understanding of who Neal actually is rather than who he wants Neal to be.