This may not be the 100% correct answer, but it is the way we've played it...
The sabotage card completely undoes the action card against which it was played. Also, as a matter of being nice to everyone else at the table, the sabotage card is played before the action card (against which it is played) begins being resolved, not part way through.
I hope someone else can comment with a definitive answer.
I can't think of any other reasonable interpretation. I believe Sabotage states "play in response to the play of an action card," so would have to played right away, thus undoing the action card in its entirety. If there was a "partial completion" to an associated action card, I think it would cause WAY too many problems in the game.
The bad news here is that "Silence of Space" probably states "play after activating an area", which means that the player that intended to sneak through an opponent's system is going to lose a CC! That's punishment enough.