I mean yes, but the whole point of this series, more or less, is sadism on the part of the player (or masochism, if you're self-inserting). It's about watching the confident hero get his shit kicked in. Also, you get to have your cake and eat it too, because there's three different ways you can have stuff play out: "bad" dead ends, the pure route where he wins, and the trained routes where he "wins."
But yeah, he's a good guy. That's deliberate and important, because it wouldn't be as much fun to mess with him if he was some cardboard character. Grinding a person down until they're just a sextoy isn't, as you put it, impactful if they weren't really much of a person to begin with. They have to have something to lose: power, dignity, friends, a potential lover teammate. But, for the pure cinnamon buns out there, there IS eventual Scratch content planned that will ONLY be available on the pure route, so there will be some actual content there and it won't just exist for the sake of contrasting the "bad" ends.