In explore route you neednt follow any rules.
if you hit tab and you hear "permission granted", you can pass and be ok, if you want to follow real rules proceed at restricting until you come to a more favorable signal, but msts interperates that as a clear i believe.
You can also alter the activity to prevent getting the red board to begin with. I could help you with that but i need a scenario first.
Aside from that i dont know of any way to prevent that but im sure you can tweak it somehow. I think you should just get an automatic penalty application, or if your locomotive is not capable, you just smash into the guy in front of you.
I will repeat the question in the train-sim.com forums for you.