You know, I think it's interesting that you read that final scene as Peter throwing Neal out of the White Collar family, because I'd read it in exactly the opposite way: that Peter openly acknowledges that Neal's part of the White Collar unit "family", part of his family, and because of that he's having to bring in someone from outside the department to handle Neal -- everyone else, including himself, has become too emotionally involved. It's basically the opposite of throwing him out: he's not reassigning Neal outside the department, just partnering him with someone who isn't emotionally compromised by having gotten too fond of Neal over the years, as is the case with everyone in White Collar now.

I don't think Peter means to throw Neal out of the family - he explicitly says he's not - but I think Neal is going to perceive it that way. I don't think he cam perceive it as anything else.

It's not so much that Neal is going to hold a grudge - he won't be angry (at least not for long) but he won't ever trust Peter again, either. (Which has less to do with Peter doing anything wrong and more to do with Neal being a giant ball of massive trust issues to begin with, even before this. That this comes right after James' betrayal isn't going to help.)

Part of the problem, IMO, is that Neal fundamentally doesn't understand the conflict Peter is having between doing his duty/doing what's right and protecting someone he cares about. To Neal, duty/what's right IS protecting those you love, period, full stop. That's it. (Also, Neal has zero concept of emotional distance/the dangers of loving someone too much. He doesn't think there's any such thing as being too emotionally involved.)

(And I have more thoughts, but I'm on a public library computer because mine is in the shop and my time is about to run out argh!)