When Vader scratches Early Warning System off a ship, does the chaff token immediately come of or does it come off at the end of the turn?

EWS has its effect at the start of the ship phase. So following how this sort of thing works for other upgrade cards, if the card is destroyed, that doesn't undo its effect for that round.

I agree with @Grumbleduke , the card specifies that the effect applies until the end of the round like the Fleet Commands for example and we know that those effects lasts until the end of the turn even if the ship where they are equipped is destroyed. So for EWS it should be the same.

Killing the guards means nothing once the alarm sounded and everybody is already warned.

?