I guess it depends what's the main hidden element you're after - You're original idea seemed to be around teams or factions. I think that's viable, you just need a way that swapping teams is a game changer, but not a king maker element.
I think if you started with two teams, say green and red (for sake of arbitaryness). What you could do at an appropriate trigger point is draw from one of the traitor cards keeping the result secret. I don't think this balance is right, but something like:
3 cards saying: no change, stay fighting for the team you're on, you win if this team kills all other players (even if you died).
2 cards saying: conversion of faith, you are now fighting for the other team, you win if your new team kills all other players (even if you died).
1 card saying: rogue element - you no longer believe in teams, you win if everyone else is dead and you, or a creature of yours is still alive. When you reveal this card add 6 points to your total life and 2 to your channeling.
If you change allegiance through a new status card, all enchantments, conjurations etc stay in play as normal (noone knows you're a dirty dirty traitor yet). When you reveal your new role (possible at the normal spell reveal stages) all spells are checked for legal targets (i.e. are your spells still attached to legal targets, friendly etc).
If someone reveals a new allegiance and you are the only mage remaining in your faction heal 8 dice worth of damage. (thought that would balance the losing mage suddenly lowest on health and no allies).
The power of changing allegiance has a powerful effect in Etheria, and all illegal spells are destroyed. I thought about returning them to their spellbook, but felt it would drag out the game.