Scully doesn't have a mean streak in canon. So if you want to give her one, you need to give enough material to the reader to justify such a change of behaviour. Otherwise you'll lose their suspension of disbelief.

This. Plus I think there's a difference between "heartless bitch" and "callous and rude". It's like Medea Scully versus Trucker Scully. (Okay, maybe not 'Trucker Scully' but I can't think of anything more fitting off the top of my head.)

he was never given a chance to just be what I think he really is: a clumsy, worried big brother.

A clumsy, worried, condescending, domineering big brother.

I guess I'm not going to be in the Bill Jr. club. I've always disliked the guy.