My theory is that Nathan's father controls pretty much everyone at the school. Jefferson likes photography, so he was the best to do the job of photographing students and doing creepy shit. If your read Nathan's father's emails to Nathan, it shows how manipulative he is and he's planning something nasty. So, in a sense, Nathan is a victim as well. Nathan's psychiatrist emailed his father and said that he needs to help Nathan get through these mental issues, but his father keeps declining. Perhaps to keep Nathan mentally unstable and give him no one to confess this disgusting stuff to? In one of the pictures in Rachel Amber's binder, it shows Nathan posing with a (possibly) dead Rachel. Maybe he was drugged too and forced to take pictures with the girls.