The pressure put on teams from sponsors if their money ends up in FIA coffers is a pretty big incentive I suggest and will certainly help to prevent teams from breaking the rules to often.
You are right, there is a financial penalty to pay for loss of points in the constructors area and this can also effect the sponsors along with the team as the lost money needs to be made up in the following year. This of course assumes the same sponsors stay for the following year.
The Drivers again need to be assessed on ability to pay, but other measures like loss of grid places or even deduction of points have their place.