What Josh said - I don't think Walternate's transformation was instantaneous, or that any of the events happened all at once. There's 15 years of backstory we didn't get.
I think what it really comes down to is what we see in that moment when Walter and Walternate finally meet each other; they're both understandable pissed (and I'm paraphrasing here) but Walter essentially says, everything I did was an accident, well-intentioned and ultimately selfish, but that I never intended for these consequences - and that you, Walternate, all of the destruction and violence you waged, that was intentional. It's an important distinction. But I think the brilliance in Noble's performance is that I can understand the motivations of Walternate as well as Walter. There's a little bonus feature on the Fox website called "Noble Intentions" where every week, they have a brief interview with John Noble about whatever the episode concerns, and it's really interesting to hear his thoughts on the characters and how he plays them.
In the end, for a show like Fringe, I find it hard to make any kind of final determination or judgment of what I think -- because I'm very aware that I haven't seen the full picture yet. To my mind (and I totally understand how others would differ, this is just my opinion), to judge whether a certain plotline or episode works at this point would be like saying a random chapter out of book worked or didn't work - I feel like I really need to see the whole before I can fully criticize what's going on. So while I reserve final judgment until the show is, well, finalized - I have to say I'm enjoying the ride. It's certainly tough to have to wait months for it to come back, and even week to week, it's not so easy waiting for the next episode. It's one of this cases for me where, if the last episode I've seen has been a little disappointing, I want the next week's to make up for it, and if the last episode I saw was great, then I can't wait for what comes next.
(There are some people or websites that review each episode from week to week, for instance saying one episode was a B+ and another was a D, and without seeing how they all fit into the larger whole, I find it impossible to make that kind of determination - and almost unfair to even try to.)
