I don't think that there was ever and incident when Grey Knights died in huge numbers and their gene seed was not recovered.
And I don't think that you can just secretly sneak onto their battle barge and blow up the whole oxygen supply so they all suffocate. Further, I wonder if Chaos can bring back sapient zombies in large numbers. If not, you'd have a force of grey knight bodies with damages brains (due to the cut off oxygen supply), so without being a real killer anymore.
Thus, I'd second the World Eater's advice - use the Grey Knights codes as an Elite force, like Black Legion CSM who were once upon a time members of the First Company of the Luna Wolves, for example.