There seems to be a number of issues with the overactive pathfinding in the game, and this is the worst of the problem but not the only one. A slightly less serious problem is that trains sometimes spontaneously change the track they use at a station, potentially causing deadlocks.
The solution is obvious, and would even make the game less resource hungry: Run the pathfinder only on demand. It is appropriate that it runs when you make a new route. When you change either the route or the track/road, it should give you a hint that you need to take action, but it should not start on its own. Only the player knows when a change is finished and ready to be committed.