Or, alternately, they have something like 50 characters on the island and the ones that don't have compelling storylines, they want to take off stage to provide room for those that do have stories in them.
They could probably keep them around, just off at the edge of the screen, but 1) they periodically need to reinforce the danger of the situation and killing someone who's "done" lets them do this without removing the more compelling storylines from play (for the most part; see Libby for an example of how this isn't always true) and 2) people would keep asking to see Shannon, Ana Lucia and Charlie, which would eventually clutter things up with "done" characters.
I don't think there's a sinister agenda here on Lost, just them trying to manage a fairly rough story structure they've set out for themselves.