That's still an assumption; we weren't there. Studio politics don't always welcome the most obvious people.
Frank is VERY busy with other projects, and while he does still pop up on Sesame Street from time to time, he has left the Muppet Show characters for other pursuits. I don't think the studio or writers intentionally left him out. After all, the writers
did go to him first with their script.
I'm starting to think one of the problems was the new writing team having to deal with the recasts. Otherwise, I don't think they would have bothered to get in touch with Frank.
Still, you have to admit how graceful Frank Oz is here. He doesn't want to ruin the movie for the fans and he's happy it's been a success and keeps Jim's vision alive, if not quite in the details he remembers/created. He could have been a complete Alan Moore about the whole thing and completely dissed the audience for even acknowledging the movie.