removing humifier control
First, you're dealing with low-voltage wiring. There's no real risk of shock or fire. For that reason you can do as you like. 

The only real risk is of a short, which could potentially damage circuitry or just waste power. However, I'm guessing that the power supply for this circuit was at the furnace, or there's a battery in the controller. Since you've removed the furnace unit, check for a battery and remove it, then carry on.