As much as I'm not a fan of Armageddon spells I don't think they should have an on/off switch. The spells being in the game are a part of the balance between the spell circles, unless of course each Element Circle has exactly one Armageddon spell.
The most direct counter to Armageddon spells is obviously Disjunction. I think Armageddon spells should be one of the auto-notify things in the game so the player does not have to check the what-are-the-other-Sorcerer-Lords-doing screen every turn.