Space marine heroes in canon defeat C'tan shards on the regular and all that Imperial-Whatsits isn't really worth much if we assassinate him with a Soul-Breaker Orb or or similar 'screw you and everything in your general direction' First Age tech.
The other advantage of assassinating someone with a Soul-Breaker Orb it does not leave witnesses that aren't insane ghosts.
That was Matt Ward era and is not a flattering era and Void Dragon is the most powerful of the C'tan shards it even by itself when unleashed ended the Rangdan War with how devastating it was and you are underedtimating Big E's capabilities for all we know he could precognition it and besides he is an amalgation of many shaman souls we may only just destroy a part of him than the whole even then it leaves other primarchs, Malcador and Valdor who won't take kindly to our assassination which no way we can keep it a secret when the head of the state is gone.
And that also leaves the issue of Imperium that spanned across thousands of worlds with many Astartes and Titans unless, this Soul-Breaker can also deal with an galactic spanning empire?
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