Hmm.

If you stop pumping bubbles through the water where does that leave the humidity? Also word of caution - air pumps can create a good bit of vibration - when I was running the DIY humidiifier I had to place the pump on a different shelf altogether because I din't want to subject the BP to all the vibrations.

Instead of a timer have you considered a thermostat for the heating? Since temperature affects how much moisture the air can hold once you get the temps stabilized (heed Adam's advice on where your cool end should be temp-wise) I'd tackle the humidity at that point. Depending on how much water the waterdish/bowl holds the placement of that can also impact humidity (placing on warm side produces a slight bump and vice versa).