I don't know why Henson got to keep Emmit otters Jug-Band Christmas (after all, Disney got Mr. Willobys Christmas Tree, which probably features Kermit in probably the same amount of screen time), but henson probably kept the christmas toy becasue it inspired a Henson series called The Secret Life of Toys. That's probably also why Henson got to keep the Jim Henson Hour special Dog City, even though Rowlf was heavily featured in it.
Even though the opening credits for Fraggle Rock read "Fraggle Rock Starring Jim Hensons Muppets", this show never featured any recognizable muppets. it was pretty much all original characters throughout the shows run (although Food, a weird-looking crature created for a Saturday Night Live muppet sketch, was seen in the episodes Let The Water Run and You can't Do That Without A Hat). The main Fraggle Rock characters weren't used much in productions that starred the muppets. Many minor characters from Fraggle Rock have occassionally popped up in various productions, such as The Muppet Christmas Carol and Muppet Treasure Island, but since these are minor characters who aren't Fraggles, Doozers, or Gorgs, most people probably aren't going to know that they were originally from Fraggle Rock.
I think it would have made more sense for Disney to have gotten Sam And Friends, Mopatops Shop, and Donnas Day (and maybe also The Animal Show with Stinky and Jake) than Fraggle Rock.