Sorry but you are wrong. Disney (or should I say the Muppet Holding Company, a subdivision of Disney) did buy the past productions of the Muppets (with a few rare exceptions). They own almost all of the Muppets works, they bought the past prodocution catalog of works the Muppet have done (re-read the press release from the deal).
The Muppet Holding Company owns the compleate rights to the Muppet Show and they are the ones behind these DVDs. The Jim Henson Company is still around the Muppets as "creative consultants" on all productions/products; so they do have a hand in these DVDs. But the Muppet Holding Company (Disney) is the one who are producting and making these happen.
Only 40% (less than half) of the Muppet Show episodes were released by TimeLife. You may have some duplicate episodes but there are episodes you don’t have. Also, it may be awhile until all the seasons are released and those DVDs will tide you over until they are (and have until now). They new DVDs won't conflict with a majority of your collection for another 2-5 years until they are all released. You can always sell your old DVDs if you are pressed for cash; or keep them as a collectors item. Also you don't have to buy the new sets if you feel ripped off.
Disney did not release the editied DVD of Emmet Otter. Disney does not own Emmet Otter. The edits in Emmet Otter's Jug Band Christmas were due to the Jim Henson Company. Disney has nothing to do with Emmet Otter.