There could be numerous reasons that JetBlue did not allow him to move. I’ll give you one issue and that is weight of the plane. You are not allowed to just change seats since they need a certain amount of weight on both sides of the plane. Usually it’s not a problem, but I have been on planes that it has been. Just because this fellow has a religious problem, they can’t just change things. Also, it is completely normal procedure of airlines to throw people off if they are not listening and causing trouble.
The security violation you mention is actually not one. The violation is leaving people on an AIRPLANE for 3 hours not in the airport.
JetBlue happens to be the most respectful of all airlines when it comes to Jewish issues and customs. There are countless stories of them allowing minyanim on planes which other airlines will not. All the food they serve is certified kosher.
Why didn’t this individual book seats together with his parents in the first place if he was worried about his parents and sitting next to women? JetBlue even allows you to pick your seats and change them free online without any charge. Why didn’t he just do that?