"The Secret Life of Toys" and "The Christmas Toy" are part of the Henson Family Showcase. The Jim Henson Company owns the shows and special, and currently HIT! Entertainment has the distribution rights (until 2009). Disney does not have a hand in the ownership of these.
There were a few rumors that in "The Christmas Toy" special, the opening and closing narrations by Kermit would be edited out or replaced due to conflict with Disney's ownership. But their has been no official word one way or another if that was true and Kermit will be gone; or if just some fans making broad asumptions after the deal with Disney.