Okay...so the dvds have cuts. This is too late to change. So the practical question is...what do we do about them? To buy or not to buy?
My reccomendation is buy the dvds. Show your support for the fact that (cuts aside), Disney did largely try to put something very special together...how long have we dreamed for season box sets with all these fabulous extras?
BUT...if you are upset about the cuts...LET DISNEY KNOW!!! Write, call, email (or all of the above). Say that you are upset about the cuts and request that Disney work harder at obtaining the stuff that was cut and if at all possible to include the stuff that was cut from this set in future sets (One thing that i don't think anyone here has brought up...it may be possible that Disney did everything they could to obtain the music rights for the cut material but were up against time...they cut have held back the release date which they figured would make more people upset. Encourage them to continue to get the appropriate clearances and get the cut stuff available on future sets.)
I will say (and i encourage people to mention this when they contact Disney) that for the powerhouse lawyers Disney are supposed to have, they really dropped the ball here. Since these episodes were already made and broadcast (and in some cases released) in other formats, they should be able to make the arguement that in being that the permission had already been granted to use the music for the original episodes, that that in itself should suffice...that the rights were granted to use the music in that episode and that should cover any and all future airings and releases. I would also point out that you mention that a precedent (and DO use that very word, "Precedent") exists in releasing the episodes uncut, reminding Disney of the Time-Life releases.
I very much reccomend letting Disney know of your displeasure. When they release something uncut once, it gets very easy to continue the trend...they may have pulled some hairs in frustration, but when it comes around to season two (or season five) they may just shrug their shoulders and say "They bought 'em anyway, they don't care...why should we work so hard?" They should know Muppet fans don't like Jim's vision being mucked with. Flood them with calls, letters, and emails. But at the same time, don't forget to be polite no matter how mad you are. Thank them for releasing the dvd's to begin with...make sure they know the specific issue you're upset with and why. If your letter is too angry or disrespectful, they will disregard them as being from a lunatic; respectful, thoughtful letters get things done (especially when they're in mass volume.)
Finally to clear up some confusion...yes when (USA) Nickelodeon aired the Muppet Show they made some cuts, sometimes juggling the order of sketches and even mixing in stuff from other episodes...but these cuts were made for the purpose of time...they didn't have (or want to give) the full 25 and a half minutes...they cut down their episodes to 24 minutes and left six minutes for commercials (which to their credit is still more than most USA networks which allow 23 and a half minutes like the original syndicated versions.)
For what it's worth, when i contact Disney, i'll also be requesting that future box sets contain the Brian Henson intros and all the promos...and ask that the intros and promos left off this set be included in future sets.