Impossible to achieve precise running times in mixed traffic? How long since you've been to Czech Republic? It boils down to proper traffic management and targeted separation by the overall agency/agencies (as well as enough padding built into layovers). Until that's done I thnk its pretty unfair to fine the operators.
It can be done with the political will. Why do you think all those unidirectional systems don't collapse in a daily heap? They have little opportunity to short shunt. It also smartens up their operational discipline. Short shunting is a pretty disgusting practice from a passenger point of view and should be avoided if at all possible.
(Who could set his watch by the trams in Prague)