Well, first of all - almost everybody here is an EX-JW. This forum is primarily for people who have broken out of the cult. Reading some of the threads here will give you a picture about how hard it is to leave this religion once you have gotten involved in it.
Aside from the JW issue, it sounds to me like both of these people have some serious life issues - in my opinion, low self esteem is just the beginning. This relationship, as you have probably guessed, is nothing but trouble - besides the fact that she is getting him involved into a high-control cult.
I would continue to research the witnesses here, and have a serious talk with this boy about exactly what he is getting himself involved in.
You are, by the way, right about something being wrong with the supposed instructions from the elders which was given to the girl - I cannot believe that they told her it was OK in any way, shape, or form to continue to have contact with your son. Probably she has fabricated that. In strict JW rules, this girl could have been disfellowshipped (JW version of excommunication) just for being in the hotel room with him alone overnight.
It is hard for a normal person to believe that the girl could both break the rules of her own religion, and at the same time try to get your son involved in it - but, it is not that uncommen because this is a mind control cult and very difficult to break away from.
Good luck, hope you can help him see the danger of this religion.
James