The main points here are that the Henson company are not selling "The Company" (as in with EMTV), they have sold "The Muppets", "The Muppet Babies" and "Bear". That includes the licensing, puppets, and past shows and films. Thats all they are selling. The idea is that Disney will hire "The Jim Henson Company" as a freelance independant production company to produce new shows and movies but ultimately Disney will control what happens and how it happens with those shows.
My gut reaction is that i don't like it at all. Loads of Jim's properties are well and truly totally split from each other now, and it doesn't sound great for the ones that have been left behind with Henson. It means they can go ahead and make new shows (like Farscape) themselves but you can imagine for something like "Fraggle" it would be harder for them to really do anything with it now. It also means the Henson's have no real control over what happens with the puppets or brand yet again, if there was a problem between Disney and Henson you could see the Muppeteers and Henson kids on one side, and Disney and the Puppets/Brand on the other. The positive is that we will now see new shows and movies, and the programming Disney buy will be seen on their channels and released to video/dvd. Overall the brand will have a lot more visibility and get more of a "push". I think it has come at a massive price though, a part ownership deal would have been MUCH better and safer. It also means that licensing wise we'll probably see a move away from "speciality" stuff (like figures and busts) back to the more kiddie stuff of the 80's and 90's, but we'll be able to get hold of it easier.
I would guess this deal was brewing even before the kids bought back the company from EMTV, and if not, could be the result of things not really working out that well financially since they did get the company back. I remember Charles Rivkin at the Sun Valley Media Conference ensuring people that the kids hadn't bought back the company just to sell it again and it seems these words were a bit misguided i guess.