Maybe except Alaba, I think Gustavo and Badstuber were rightly shown yellow card. But the system is indeed flawed. A final should allow the teams in their full strenght. It is probably that Bayern will request such thing after they tried to do with Ribery in 2009 and Beckenbauer fighting for players not to be injured in national teams. However, even if UEFA decided to do such change, it couldn't come in effect in the currently played year.