In April 2008 the four-year consulting arrangement with the Jim Henson Co. will end. Until April 2008, Disney is obligated to work with Henson to get strategic advice on the use of the characters. This was to help keep the character integrity intact for the transition and to help the new people treat the Muppets "right". After the consulting arrangement ends Disney can either a) renew it and keep working with Henson for advice and overseeing; or b) they can stop working with Henson and make their own decisions on the characters and production plans.
In April 2007 the three-year production deal to develop movies and television shows ends. This means until 2007, the people at Henson are obligated to help with the production and development of new movies/TV shows. After 2007, Disney can choose to keep working with Henson to make Muppet productions (which seems likely as of now; unless Henson does something to tick Disney off). But come 2007, Disney could choose to develop and produce things on their own, with a diffrent production company.
After these deals are up the characters, ownership, and control stays with Disney (they bought the Muppets), these were set up to help in the transition period. Henson was legal obligated to help transition the characters and continue to support, develop, and oversee things while Disney got to know the Muppets. This was to help Disney get a proper persepective on the characters, productions, and works; without the Muppet world coming to a hault for the new owners to get onboard.
Even after 2008, its pretty certin that the two will still work together. It is unlikely that The Muppet Holding Company will break all ties with Henson (even if it is just to make puppets, film productions, and gain access to the archives).