Ok, so I'm officially a derp. I always took it for granted that because Nea died that the half of him that was the earl would be claimed by Mana.
BUT! considering how emotionally unstable Mana still is, it's actually more likely that they both need to die in order to become reborn whole.
Nea wants to kill Mana because whilst he is still alive, they can not go back to the way they were always meant to be.
He still loves him, but he knows what must be done.
I can't believe that I'm only working that out now.