For the combat classes, I sort of agree, because there's literally no difference in what they can do. For the gathering classes, no, the restriction actually makes sense there (you shouldn't be able to get basically free gathering stuff if you don't have the appropriate class leveled).

About the only reason I could see the restriction for battle classes still making sense would be if, at some point in the future, we can take along our retainers as companions, much like our trusty chocobo.

Oh, and you can always reset your retainer's class. It'll take a bit for them to level back to where they were (depending on how high you have your NIN), but it'll probably be less effort than to level a class you don't want to play.