Send Evil Troy back to the hell that he came from! Oh, wait it's gone already?
My interpretation of the rules is this:
When you select a Spawn Zone to remove you have 2 choices:


A regular Spawn Zone (not a Necromancer Spawn Zone) 
The Necromancer Spawn Zone for the defeated Necromancer


In the first case the Necromancer Spawn Zone for the defeated Necromancer becomes a regular Spawn Zone.

This means you cannot choose the Necromancer Spawn Zone for any other Necromancer currently in play. Thus, when Evil Troy is killed, his Necromancer Spawn Zone should still be on the board.