It's not possible currently. The game creates a list of respawn points at the start of the mission and will continue to use those points in space regardless of whatever happens later on in the mission (although it will check that the ship isn't respawned inside the bounding box of any other ship).
Since running into a related problem when making missions for BtRL I've been thinking about adding FRED definable respawn points to the game.
It might be possible to fake it by moving the ship as soon as it respawns by using the set-object-position SEXP. Figuring out how to do that though is a rather difficult proposition though given that you probably won't be able to use the is-destroyed-delay SEXPs after the first respawn.