Well, I'll try to give you some insight as much as I can but I'm afraid that if you don't like the raping theme and enjoy being challenged by a game then Karryn's prison might not be for you friend.
Now, about the combat... You level per your actions, so let's say you're always using that blunt skill, you'll level Strength. So you have to be careful when and how you fight depending on which kind of build you are going for. If you would like to go ''warrior style'' I suggest building more Dexterity as it allows you to hit and crit more easily. Also, maybe aiming for a +10 accessory might help you out. If you like the game and would like to steer away as much as possible from the raping mecanic, try playing on secretary mode. Enemies are easier and it is more forgiving. So in essence, levels are more an approximation or where you are compared to the level limit you have for each floor.
As far as the thugs are concerned, their special attacks can down you if you're not using the defensive skill to prevent that from happening. I don't remember where in the thread, but someone posted a very detailed walkthrough for many routes. If I stumble upon I will link it to you.
Now, about Melty's quest, you can avoid pretty much everything you want if you play on the easiest difficulty, but yes, raping is pretty standard in that game too if you play on the hardest difficulty available.
I hope this helped you. Take care.