sPzAbt653 is correct. Set the rail repair to 0 in the events, and the only repair will be via RR repair-capable units.
I'm playing Telumar's Anzio scenarios and he has the events set for both sides. There's a hex pre-determined to be 'damaged RR' at turn 1, and unless the German player gets that far with his RR unit, it stays damaged all thru the scenario. Allies do not have a rail repair capable unit. Note, in these scenarios (1 KM and 2 KM) rails are not damaged when a hex changes ownership.
In Snefens's Operation Neva, 'automatic' rail repair is set to 0 for both sides in the events. In this scenario, hex ownership change does damage rails - actually just having a partizan unit breathe near the RR seems enough to damage RR. And both sides have RR repair units, management of which becomes a sub-game all in itself.
HTH