We should remember that Jim Henson was selling the Muppets to Disney before he died. I know there was much fall-out after he passed, but he really dug the idea of the Muppets being under the Disney banner. Of course he would have had some say in the projects.
I also feel the Muppets had lost some of their shine before Jim Henson passed away and that the Disney deal was going to help boost them back up.
On another note, I have heard that MFS was plagued with more problems than have been reported. And that was, as stated, Sony (Columbia/Tri-Star). I feel MFS is the perfect example of feeding a project that just isn't working. If Disney is trying to keep that from happening (as I think they might be) than I'll be patient.