Johnny loaded Ghost's save in Skyrim and killed Parthurnaax, so Ghost had to kill him.
If i were ghost i would've just evicted him from reality. Not just killed him, but kicked his ass out of reality. I would've not just banished him to the incomprehensible depths of nothing, but erased any mention of his existence whatsoever. I would've broken the very laws on which our universe stands on, just so i could erase him.