I'm afraid that I must add my name to the list of the baffled.
While the TOC can do as it wishes, it does seem to be a very strange thing to have chosen to do. A train reporting number is not something that the general public will even be aware of existing, never mind having any attachment between an alphanumeric code and an incident. It certainly appears to be a strange way to pay respect to the deceased.
As for the reactions of rail workers, my own feeling is that this has been overplayed. I very quickly forgot the unit number, headcode and even the service I was in charge of when I had a fatality; currently my most traumatic railway experience. These details never entered my head and I certainly never had any flashbacks nor unwanted psychological reactions as a consequence of seeing a certain unit or mention of a certain service. While we all mourn the loss of colleagues, and those who work for ScotRail more so than others, the number of staff directly involved in this accident is small and therefore any psychological effect will be localised. To retire a headcode entirely within the region on the grounds of psychological harm seems a bit over-the-top.
But then, these are just my own thoughts and feelings on the matter.