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Perhaps there should be a mortal incarnation of this Dark One... a necromancer or lich king of some sort that the Lightbringers could expressly find and target, instead of accusing each other of being enthralled?  You'd need to keep him or her hidden for that reason.  Actually, being a lich king/queen could be especially interesting, in that you'd need to make and hide phylacteries that the lightbringers would want to hunt down.

Or, if you want to keep the lose condition simply being a turn-counter, you could make it so that raising undead armies requires a focus of some sort that the lightbringers could find and destroy to destroy your whole army at once.  That'd be a major setback, after all, making the timer a threat.

Making some kind of core to the undead empire could be a useful addition. Currently the issue is that the undead are incredibly unbalanced, due to their nature. At first they're incredibly weak, because there aren't enough bodies, then they reach a point where they can make headway and suddenly there are unlimited dead bodies to form new armies, and you win almost instantly in an exponential zombie cascade.

Having a core would give something for the lightbringers to attack, like you said, and give a reason to slow down the undead spawning, perhaps tying the max undead to the size of your empire's construction. I'll have to play around with it to see.