Haven tactics.

I'll probably try it... :)
If there's only a small group of REALLY UNKILLABLE cyclops left, you can cast plague on them and run around the map, avoiding them.

It's not that easy to run away from large creatures. And besides, there's not much anyone can do (except in cases where there's an artifact that increases speed, the "death march" perk, or a castle siege happening at the same time :). And if the cyclops are bloodthirsty and have a speed of 6, then there's no chance. Unless you try to escape with griffins using the "strike from the sky" ability, but even then, you'll eventually get caught. By the way, teleportation can also play a decisive role in "escaping" from cyclops, but the spell might simply not be available.

Furthermore, mind control works on cyclops, but only if the enemy doesn't have immunity to mind control, and your magic skill is at an expert level. In a pinch, you can try to mind control executioners – they're pretty fierce.