Mullally's departure has nothing to do with the alleged pay cuts, from what I understand her new pilot with Alicia Silverstone was picked up by ABC for mid-season so she must leave to work on the new show.
"Some people can thrive and bloom living life in a living room, that's perfect for some people of one hundred and five. But I at least gotta try, when I think of all the sights that I gotta see, all the places I gotta play, all the things that I gotta be at"