The short answer is that her character left "to pursue other opportunities" and such opportunities seemed to be unavailable within the show.
Let's face it, the Catherine character was one of several comedy foils for the Phil Hartman one and they didn't ever figure out what else to do with her. At least they allowed her to walk away under her own steam and even return for a cameo if I recall. I might be wrong but I think that in real life Khandi had something going on in the upcoming pilot season or perhaps a recurring role or two in some medical or police procedural drama at the time.
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