I have not done coil, which is not part of the MSQ anyways, but I thought Nael was dead and the one we fight is an aether version.
I mentioned Moenbryda, and neither her nor Nanamo are removed from the story, their deaths serve a purpose in the storyline, and they will still be part of it even if not in it, though Moenbryda may come back.
Gaius' death was not to remove him from the story, he is the guy we stop from enslaving Eorzea.
So none of the death's were for the sake of removing them, they all serve a purpose in the story. Even Wilred's, and the sylph's death after the storyline Titan fight had purpose.