When discussing the motivations of meta characters I like to think about things on multiple levels. For Bern in particular we have her existence as the witch of miracles, and what that represents. We also have (Higurashi Spoilers) the fact that she is all the Rikas that failed. That was her hell of a logic error and it makes her spitefulness make sense.
But another important view to consider is why she is in the tale Ikuko and Tohya are writing. Bern is based on Ikuko’s cat, so some parts of her mischievous personality come from that fact. But that also places Bern’s role on Ikuko’s side of the Ikuko-Tohya writing relationship. Bern’s role in the story is that of an antagonist. It’s a necessary role for both Battle and Ange. You could say Bern’s villain-hood is a necessary evil.
So that begs the question is she like Evatrice, playing the bad guy for the good of others, or is she actually that cruel? Well that was the original question I guess, and all I did was present a potential reason for her to have not been that cruel.
However I’m inclined to say she really is like that. The story gave no indication of redemption like it did with basically everyone else. Her cruelty was a necessary part of the equation, but it was not an act.
It is worth noting that in a different scenario Lamda could have been the bad guy and Bern the good guy. Lamda has shown just as much tendency to cruelty and opposing Bern was in no small part part of her motivation to help everyone at the end.