Mod suggestion: Seperate the 'anti-stellar manipulation' abilities from the 'anti-warp point manipulation' abilites. These two functions ought to require different facilities. This would have the effect of making it a little harder to completely lock up a system. You'd have to build TWO very large and expensive facilities.
And at the same time would make it a bit safer to temporarily scrap your warp point lock in order to venture out. If it were less risky, people would be more likely to do it, and so break the stalemate that these abilities can create in the game. As it is, all the enemy needs is a warp point opener constantly trying to get through as Geo described, and a sun destroyer waiting to exploit the loophole. Ouch!
Of course, tossing a few mines on any stars in the system would help with that situation, too...
In a game without the 'warp points can be located anywhere' option you could even sprinkle mines in all the outer-rim sectors of the system before you actually scrap the system shield...