Solution: Create a way to set a train speed limit for certain sections of track. It would probably be tied to the signals system so that it can be implemented on a per-block basis. Just add a pop-up when you click on a signal and give it a some radio buttons for various speeds. This gives the player some control options.
edit: To overcome the UI limitations (the need to zoom out; max screen resolution, etc) there are two other suggestions that have been raised:
- Show an icon at the edge of the screen on sections of rail where a train is approaching, as per sillyfly's suggestion.
- Add a warning light object as per ssilk's comment.
Safety first!