This may seem odd, but I believe the way to fix this is to correct the auto-manual behavior. If the train started in manual mode when ctrl+clicked, then once it reaches its destination and the 5 seconds expires / stop is deleted, shouldn't the train return to manual mode? If the user is riding the train and ctrl+clicking a destination, and that train had no schedule other than the temporary one, it is expected that the user would likely wish to manually drive the train once they arrive, and returning the train to manual would help with this while also no longer breaking the artillery.
I have a save with the artillery train in the 'broken' state, not firing while there are flashing x's on the minimap, but it's on the Nauvis Post Apocalypse map, so I'd rather avoid trying to share a 500MB save if at all possible
