I admit that I haven't paid full attention to ALL of the scenes... but, unless I'm mistaken, most of the rape-iness comes with the girls that are, for the most part, enemies, and it's part of the process of turning them to the 'good' side. Y'know, hentai logic. Even with the good girls, the rape-iness seems more like a thing to give THEM an excuse to fuck like they actually want too... because Japanese cultural differences, Hentai logic, and women not being supposed to actually want sex. There are exceptions, like Dai Toren being an open slut... but the girls don't really seem to mind all that much. Then there's examples like Morrigan who's quote sums up a lot about the game's logic "Even if you're rough, I know you care. From now on I will be your toy."

As for cute monster-girls... Lord of Valkyria had them, but, that one got shut-down because people were losing more and more interest in it. I don't know of any others, but I haven't played every Nutaku game out there. Quiz of Valkyria might have them, but I may be mistaken. Anything else, I don't know.