I seriously think that was the case. Lou Reed came off as one of those artists who wanted most people to hate his stuff, or at least be disturbed by it. Maybe Metallica didn't see it the same way, but they did a good job making it seem like it.Since the story was quite disturbing, maybe the point was to disturb the listeners with the music as well?
Though it wasn't very clever and came off as rather forced at times, and I think that's where the album failed.