It's probably a healthy thing for both of them.
Even better for the team. As a father,I know how protective you can be ,even when you don't realize you're doing it. Some one points it out and the first thing you do is get defensive about it. All it would take is one player complaining about it and you have an issue. It could easily blow up from nothing.
To counter that, it would be very exciting and enjoyable to coach your son at the college level and watch him succeed in your program. Going to a BCS game together would be unbelievable.
Still I think it is a good thing for him to get the experience of college ball under someone else though.