Using engines improperly should cause damage, or have other penalties

I have a couple of vizzy scripts that end up using engines in a very bad way. They will fire them, turn them off, rinse, repeat. They pretty much use pulse width modulation to control thrust. This shouldn’t be allowed, I should have to control the throttle more carefully because either:

1. Firing up the engines too often causes damage to them, and eventually the fail.
2. Firing up the engines takes time, and makes it impractical to use this approach.