Admissions (thank goodness it is not) I would simply ask why it took you 6 months to tell us you weren't going on a mission. Had you called in the first couple of months we could have changed the number of people accepted...etc to try and accommodate you. Instead you didn't respond to anything for 6 months and we assumed you were not attending our school.
I agree they can try and work with you, but your son has now been off of school for an entire year without any deferral reason. In their book does that make him a new application? It sounds like it does.
It is a very different situation than I forgot to turn in my mission call as proof of deferment. It is instead you wanting a deferral for a year when there is no reason for it (again I get your situation). So not a lack of forgetting to turn in paperwork but not doing what you and the school agreed to altogether.
I wish you nothing but the best and that it gets resolved exactly how you want it. I just don't agree with you putting the blame on this one at the admissions feet when you "ghosted them" for 6 months.