I like Rebecca being Malevolent so I decided to let my girls have some willpower and found out I liked it better that way. Sure they get a little uppity sometimes but then I get more satisfaction in punishing them for it. I like the other bonuses too.
Malevolent is nice if you intend to have your girls fight with you for longer than it takes to get to 20 respect (or especially if you have her earmarked for the arena). I'm not sure it serves any purpose otherwise though besides screwing up the mood for everyone else in the house.
For bondage purposes I like to kind of rotate which girls are the 2 main slaves and leave morning blowjobs on until they've all refused often enough to get a few points of defiance. Then you have an automatic success for getting them into bondage without screwing up their mood at low skill levels.
As far as willpower I think I want most of my story girls to end up with high willpower eventually. For game mechanics reasons I do prefer to break everyone initially to train discipline and skills up easier. Then I can boost their willpower back up again. Randoms I'd rather just keep negative forever (or until I sell them or turn them in for the dockgraves quest).
As far as seduction vs bondage, I find that early in the game I kind of need to do seduction first because otherwise I have to force her and she ends up despising me. I'm not sure if you can improve her mood if you just keep fucking/whipping her that way or not, but I just find it too disturbing to play as a sadistic fuck like that so I haven't tried it. I do find that once her affection is up around amiable, bondage seems to do a better job of boosting affection than seduction does. Seduction seems to be better at boosting happiness and reducing willpower from what I've noticed.
I've taken to spending a lot of time whipping the girls at Dockgraves early in the game now since it's the only reliable way besides books and the bondage class that I've found to raise flagellation. Flagellation is pretty much THE skill to raise affection once you get it high enough to not fail at it constantly.