Is this to be a multplayer game or a scenario? If it's a multiplayer game you could do similer to Dogscoff's sugestion, but have a non-player player control the warp opener/closers. This would allow you to have more conrtol obviously and make sure they get closed.
You could come up with some random method (dice?
) to determine if a warp point is to be opened, and then come back after a predetermined amount of time and close it.
The players would either have to ignore the ships doing the manipulation, or you could work up a little mod that would give you a racial trait with say a opener/closer/level 6 cloak/level 6 scanners(so you can avoid the players minefields)/no maint component. Then build a few of these and run them around the quadrant doing your thing while everybody else plays the game.
Geoschmo