It can be a bit of a hedge. They can start out with a new character who steps in after Kate disappears. If that works, Kate can stay gone. If it doesn't, they can always bring back Kate as a recast character.
In comic books, it has become common to replace a character with a new version. Everyone knows the classic character will eventually come back, but the success of the new character may determine how long they wait. Examples from comics include when Batman's back was broken and when Thor became unworthy to wield Mjolnir.
Of course, in the genre, disappearing isn't necessarily better than dying, because characters come back from the dead all the time, but taking the character off the table in a way that allows her to come back, whether it is a mysterious disappearance or an apparent death.
I could come up with several ways to work around this issue, many of which would be copying things that have been done in comic books. The problem is that every potential solution is going to piss off some segment of the fans.