Well, I'm not too fond of this VN too. But I think this ending is still better than Code Geass'. Wait, that's not a VN, was it? Well, whatever. The point is the creator actually made the story to be so. If you read it more carefully, you'll understand that their world is not "the real world". It's a world created by the protagonist to be his safe haven. But in the process, he dragged several people inside. So the existence of Nanaca in there isn't strange, it's just the feeling hold by a mother who worried about her son. About him being a "monster", you could see the examples of why on Hollywood movies. Even people who in a glimpse look the same as the others, are "monsters" if they are far from being "normal". People tend to be in a normal state, having normal life, normal friends. Then they usually call a person who doesn't fit these normal states, "monster".
In the end, the protagonist decides as a monster, he could only and should live alone in there, and you got the ending.