The Electric Company box set featured a few appearances by the Road Runner and Wile E. Coyotie, who are owned by Warner Bros., which is almost as big a company, if not equally as big, as Disney. Of course, WB might also have different feelings towards licensing it's characters (after all WB did license it's Looney Tunes characters to Filmation for Daffy Duck and Porky Pig meet the Groovy Ghoulies, to Touchtone for Who Framed Roger Rabbit, to whatever company produced Cartoon All-Stars to the Rescue, and to a few other companies... and how often has Disney licensed it's classic cartoon characters to other companies?).
Having said that, the following Sesame Street DVDs that were first released after Disney bought the Muppets did feature appearances by Kermit:
What's the Name of hat Song? (though I think this was completed and a deal was finalized before the sale, as the credits mention Kermit being owned by The Jim Henson Company)
Learning About Letters
Learning About Numbers
The Street We Live On
A Celebration of Me, Grover (technically the only new production on DVD made after the sale featuring featuring Kermit clips)
Big Bird's Story Time
Sing Yourself Silly
Friends to the Rescue (though this appearance was already licensed by Henson, as it was made after Henson sold it's rights to the Sesame Street character, so I wouldn't be surprised if this was easier to get permission to release, as Hensons residuals for guest appearances by Muppets would have probably been swithced to Disney)