I think the problem, seen from the company's point of view, will be that to allow it for this man, now that it has been complained about and thus brought to their attention, will set a precedent for others.  Before the complaint had been made, they could claim that they didn't know about it and therefore it hadn't been authorised. Now that it has been brought to their attention, they must deal with it in accordance with their policy because, when a future situation arises that is less petty, they could be taken to a tribunal for discrimination if it can be pointed out that they broke their own policy by doing nothing in this case.

When Jan says....

Someone could be really good at their job, a caring hard working person (whatever their faith) and end up losing their job just for having a symbol of their faith  in their car or van

...I don't think that is quite the point.  The man isn't losing his job for having the symbol of faith in his car or van, he is being disciplined for refusing to remove the symbol of faith, when asked to do so, from the company's van, and, from the company's perspective, to do nothing at this stage, would expose them to legal action on other issues in the future.