
I kinda think that Jonas's parents are part of the order and they later on went against the order and so the order decided to eliminate them. Perhaps Jonas is one of the chosen children like Bree and he was chosen to do a certain ceremony, but his parents grew on him and knew what the ceremony was about.
Or it could be that his parents were just plain part of the order and they rebelled against them and Jonas didn't even know that they were part of the order or maybe he did, but he forgot. Maybe his nanny was part of the order also... =o She could have been ordered to erase his mind about what he knows about the order! Since his parents turned out to be such a disgrace to the order, the order decided that because he was a son of these parents, they decided he wouldn't be a good loyal servant, so they decided to brain wash him and he doesn't remember anything, but what the order lets him to know! =oooooo