She has only been out of one book the entire series. Jim needed a way to shelve her for awhile or permanently but also give her an out worthwhile of her character.
While it's true that she left the city in the first chapter of
Dead Beat, she's been shelved for most of the book several times.
Grave Peril: She's barely in the story because she's put to sleep.
Summer Knight: She gets injured after only showing up a couple of times.
Death Masks: She introduces Harry to Butters, goes on "vacation," and Harry talks to her on a cell phone once.
She's pretty involved in BR and from PG to SmF, then she has a medium sized roll in
Turn Coat.
And in many of the books she's been highly involved in, her involvement in the action hasn't been the main thrust of her contributions.
My point is that Jim has repeatedly been able to keep her on the sidelines or out of the action in the past without killing her. He could have done it in future books. Especially if Harry is starting up a serious organization. Murphy could have been extremely useful for helping Harry administrator that. Especially since he has about zero experience running anything larger than a squad.