It's a good editorial, though - as coby pointed out - a little pessimistic. There's a few assumptions Annika made that I don't think are necessarily true:
1. Merchandise
I don't think the quality of Merchandise will necessarily suffer under Disney, though it could. Disney is a mass-merchandiser. They will want to expand the market for Muppet merchandise. Will there be some horrible children's products? I don't doubt it. But it won't be all bad.
The collectible figure market is exploding and if the existing Muppet line(s) are making enough money for everyone they'll keep it going. We should also remember that to be fair - despite the JHC's reputation for quality products - the Muppets put out their fair share of lousy merchandise in their heyday.
2. Muppeteers
The JHC really only held a workshop every few years, and then only if they needed people. It wasn't done just for the sake of furthering the art of puppetry. Fortunately part of Jim Henson's great legacy is that he taught many, many people who will of course to teach others and so on. Also, they've retained the Creature Shop and other non-classic Muppet brands so presumably they will not be abandoning puppetry outright but moving towards projects like Farscape and Jack and the Beanstalk.
3. Muppets without Muppeteers
I'm not so sure that the `89 talks with Disney broke down just over Muppeteer ownership of the characters. I believe that was just one in a series of issues that were problematic. I do agree with the principal of respecting the tie between puppeteers and their characters, but this line has already been blurred by younger performers taking over characters like Piggy, Fozzie, Rowlf, etc. I think the situation is different now than it was 15 years ago. The esthablished performers are older, less available and Richard Hunt and Jim Henson have of course passed on.
I don't think Disney will be having a different puppeteer do a characters all the time. The Muppets will probably be treated the same as Goofy or Mickey who have only had a small handful of voice actors in 50+ years with each usually continuing to do the character until their retirement or death. Lets also remember that most of the puppeteers used in Disney's puppet TV shows were trained by the Muppets. I think the quality of the puppetry won't change much.