It's important to remember that this is the MCU continuity and not the comic canon/history (even if they are using that source materiel as inspiration, that is all it is... inspiration). Moonstone hasn't shown up in a Captain America movie so there is no reason she couldn't be Carol's enemy from the start. Captain Mar-Vell isn't getting his own movie and isn't going to be a main hero in this Marvel continuity, so there is no reason why he couldn't be turned into a supporting player in Carol's origin and not the the other way around. Even if Carol initially inherits Mar-Vell's rogues like Yon-Rog to start, that just means she is taking care of his unfinished business. She is a legacy hero, after all. That doesn't mean she has to be diminished, because she can still own the role and make it her own and take it forward.