The whole house Honeywell 509 Humidifier was installed and the drain run to the AC condensation pump. After a few cycles the pump no longer works. The water from the Humidifier is extremely hot. Could it have damaged the pump?

Quite possible, the impeller or float is probably plastic. You could possibly drain it into a 5 gallon pail and connect an overflow pipe into the pump. At least that way it cools a bit. Another possible solution is to see if you can run it into a laundry tub.