I think Saban is right.
It's more fun to say he's a whiner because it does look like sour grapes and they've been successful, and also 17 Bama while we're at it. I hate those guys. However, you do expose players to greater risk when they play 16 games worth of plays in a 12 game season.
Also, it's more physically demanding to play defense than it is to play offense. That is a fact. So I'm not sure it's entirely fair that the offense can determine when a defense can substitute. I think the 10 second thing was a good compromise (after all it would have affected less than 1% of the plays for most HNUH teams). If you aren't going to go for that, don't complain when guys get "injured" just so they can come out of the game.
You can't have it both ways. You want to game the system and control the defensive substitutions? That's fine, but don't complain when they game the system to get some fresh bodies in there.
Last, the refs aren't 17ing ready a lot of the time. That's just true.