I actually never thought she was that rare, since it wasn't hard to get her back in the 1990s when there were other ponies like Blue Ribbon which at that time were much more scarce. Maybe it's changed or maybe I'm just assuming.
I never knew any of the stuff behind her story, either. I don't actually own one, she belongs to my sister, but all I knew was that CeC was a restaurant over there and it was some kind of promotion. I always knew about her because DV but she's one of those vague weird things that happened in the US to me.
I agree that taking off a symbol for the reason of aesthetics is not a good thing to do. But if you were to find one with a worn symbol then that might be different. It does partly depend on her rarity, but I have a small moral issue with buying something you don't like and permanently changing it when there are people out there looking for it in its original state and the number in existence is finite. Better to save that money for something you really want, and let someone else who really wants the pony have it and appreciate it.
It's just not good collector karma overall to damage something that someone else in the community might be really looking for.