I understand your concern!
There are two reasons I’m calling her Derpy: first is because she was referred to as that in the show, so as far as I can tell that’s her “canon” name. Since the controversy I’ve noticed they leave her name off a lot of merchandise and just have her nameless (which is understandable, if a bit odd), so they haven’t renamed her since her appearance as far as I can tell.
The second reason is no matter what I call her, people are going to see her and think “that’s Derpy”. Her name already has some pretty deep, solid roots among fans and I don’t think anyone at this point would be able to uproot them. I think if I did rename her I’d get a lot of people being confused? I dunno.
Anyway, I hope that helps explain my reasoning! You definitely shouldn’t feel guilty for asking, it’s always good to address things that make you uncomfortable! I sincerely hope you’re able to enjoy the comic despite this.