And to make something clear here: It is not my intention to have mapped every track that was once somewhere.
For example here, an abandoned yard: https://www.openstreetmap.org/edit#map=18/33.80652/-84.45231
All side/yard tracks were removed, and a part was overbuilt. I deleted all ways on the overbuilt part, and left them were they aren't overbuilt. It would get too crowded otherwise. 


Suggestion for a compromise: Leave abandoned main routes only as a single way (which shouldn't disrupt anyone), delete all overbuilt side (spur/yard) tracks.
I think this is a fair solution for both sides.