I've tried to avoid getting involved in this, because quite frankly I don't see it as being an issue. To set the record (fairly) straight:
Inquisitor is not for _beginners_. It requires a deal of gaming, modelling and painting experience, plus considerable commitment. The idea is that Inquisitor is not the first game you pick up from our stores, it is not an introduction to the hobby, first time players are much better off with the more structured rules in 40K and Warhammer.
If you look at this in a literal way, this does mean younger gamers, though I'd say the same applies to a 30 year old who wandered in for the first time as well. However, I have no doubt that there are a few younger players who have been playing with toy soldiers for a while (and possibly roleplaying) who will understand Inquisitor and have the maturity to approach it in the right way. I can't comment in the case of your son, as I haven't met him (have I...?). How individual managers and clubs approach dealing with this is up to them, as far as I'm aware our 'policy' is to discourage younger gamers (early teens in my mind) and steer them towards the 'simpler' 40K and Warhammer. If they insist, I would of course let them play as long as they aren't disruptive. In some ways it is an excellent game for youngsters, as an adult can write the characters and scenarios for them, they get to play an heroic Inquisitor without really having to worry about the rules. I fondly remember by first games of D&D run by my dad when I was just ten and consequently was probably a big hook for me ('roll a D20, try to score a 19 or more. Now roll a D6...').
As ever, blanket rules always require exceptions, and I think if you actually spoke to the guy involved and explained that your son had read the rulebook and understood what the game was about, something could probably have been sorted out. But then again, I'm an eternal optimist :)