It's been years since i played an evil run, so you can probably get better answers than mine, but i'd say that the origin is mostly about the early game play style and the type of content you are looking for or want to avoid. For example the Farmer and Noble origins are famous for a certain fetish.
The only thing i can think of are the two swords you can get with a good MC which can give an edge (pun intended) to origins that can use them right away, but even those weapons can be given to companions or you can mix into a class that can use them by that time anyway.
This game is absolutely massive and there is no shortage of content and options to affect your morality, so you can play around however you'd like to.
