Air France, Lufthansa, airBaltic & SAS already said they would not fly over belarus anymore

Obviously, the next step is to make it illegal to fly over Belarus.

Or prosecute airlines for endangering pasengers by doing this.

Or refuse to approve any flights with flightpath in Belarusian airspace.

Sure, but since the EU nor the companies within is trying to emulate the Great Land of Freedom, companies won't fly there if most of the EU leaders just agreed that they shouldn't. The risk of going against recommended action and getting penalties themselves is much higher than any potential benefits of continue doing it.

Possibly, I think it will depend on how individual countries implement the directive.

I think irrespective of that if airlines ignore such a directive then they'll be exposing themselves to a significant amount of liability if something happens again (i.e. the airline will be made to pay out damages and their insurance probably won't cover it).