Killed Enzymes in Yogurt
Why not just add more enzymes after the stuff cooled sufficiently?

Enzymes you add to food are generally not toxic. If you denature them by getting them too hot, they don't usually renature spontaneously when the food cools down. They'll just act like a gram, or whatever amount, of protein added to your yogurt mix.
Adding fresh enzymes once the milk is cool enough won't hurt anything. Those new, happy enzymes will just do their enzymatic thing, and give you the yogurt you want.