Even the Muppeteers can laugh at themselves. Even though SNL has made fun of the Muppets (and Conan, which is also in the same building and many Conan folk have worked for SNL including Conana, and many SNL folk have worked for Conan) they still can take a joke, and know it is in good fun. In my opinion, none of the Muppet jokes made by SNL (or Conan) have been crule or disrespectful. Although irreverant and off-color; the jokes are all in fun and some would say it's an honor or tribute (like a roast). Even I have been known to make jokes about the Muppets and I don't hate them one bit. I think the Muppeteers understand it's a joke and would not hold it against them; plus who would pass up a chance to be on SNL?
Although none of the Muppeteers from last night were ever on the original SNL skits with Jim, and hardly any of the SNL staff from that era is still around (I think some of the producers are it); you can still feel the love the SNL'ers have for the Muppets. I hope the Muppets can return to SNL in the future, and maybe even one day host. I think that the SNL'ers really respect the Muppets, even if they do joke about them.