I'm certain Disney will make the picture with Segel. The real question is the amount of tinkering they'll do and whether they'll try to enforce a sort of Disney formula? I'm sure they'll try to push some endorsements in there, but the Muppets can handle a little bit of the "Sell! Sell! Sell!" I think. Just hope it's not too much.
It appears that Disney has been allowing the Muppets to kind of go their own way for a while. This is smart. The Mouse has never quite understood the appeal of the Muppets and it appears they are interested in learning from the characters and performers rather than shaping them into something they understand.
Every script has countless revisions. That's a good thing. From the pitch I think Disney is just letting a fan do what he sees fit. The fact that Segel is drawing on past successes and classic material should likely please Disney brass. They understand classic appeal.
One concern I do have is in the special effects department. I don't want CG Muppets walking around on screen, but I do think some computer compositing and a bit of animation tweaking for some wide full-body shots especially in musical numbers could enhance the picture if done right. I hope that's at least being considered. The Muppets have always been about traditional physical puppetry at their core, but Jim never shied away from using modern technology (including computers) in the mix. He encouraged all things.
By the way - does anyone remember that old Henson CG Muppet experiment clip that was bouncing around online a few years back? I believe it had Kermit running across a field with Rizzo running under foot. It was kind of weird, but I'd love to see it again but haven't been able to locate it.