A timer is actually a good idea. Those humidistats typically connect to the furnace in such a way the humdifier or exhaust fan will only turn on when the furnace fan is powered by your thermostat. In addition many humidifiers also have a function to only activate when warm air is being pumped through the furnace. So my point is those humidistats aren't really designed to work alone, the furnace typically also contributes to the control which prevents them from turning things on and off too rapidly.
So if it were me I'd wire in a timer to control the duty cycle, this wouldn't eliminate the purpose of the humidistat it simply mimics it's designed purpose. You could also just wire it into the furnace so it only turns on when the furnace turns on which would eliminate any negative pressure effects, not that there would be.
An alternative would be a different controller, something like this is probably better suited to the application:
http://www.canadiantire.ca/AST/brows....jsp?locale=en