The Wizard of Yendor can only use Double Trouble once per reincarnation.

Make the Wizard of Yendor naturally magic-resistant, so that he cannot be defeated trivially by a death ray, but compensate by removing his Double Trouble ability. The current state of affairs is somewhat like a lottery in whether you will be facing him with magic resistance or get unlucky enough for him to duplicate, leading to a lot of variance in how hard the ascension run is.

If the Wizard of Yendor has magic resistance and is immune to death rays, he will never cast Double Trouble.

The Wizard will only cast Double Trouble if he has already been killed at least once.