I also bought Night Trap at full retail price when it came out. I remember playing through it with my dad.
First of all, I'm sorry. 
Second, how did your dad react to the controversy about it later, given that he played this game with his kid?
I don't know, I don't remember hearing about the controversy at the time. I think my parents figured I was intelligent enough to distinguish a game from reality.
Even then, I still don't think there's anything really objectionable about the content of the game at all (other than the horrible acting, dull gameplay, etc). The whole premise is that you are supposed to be saving these girls from random attackers who will somehow hurt them. The fact that there is a scene or two hinting they will actually get hurt if you fail seems like a no brainer. How else would you be able to make the game? Plus the actual scenes were no worse than anything for some crappy made-for-TV movie at the time, anyway. Just a big part of the whole anti-gaming witch hunt, or some marketing ploy by Nintendo.
