Krista,
That is a great question, with two answers! The first is to agree with your call to have one parent taking boys to the Pirate's League, while another hits Bibbidi Bobbidi Boutique with the girls. Then, when you are all having lunch together, everyone gets to show off their new attire!
For my family, however, the answer would be no. That is because my wife and sisters-in-law would never want to miss out watching the boys in the family going through their Pirate paces, and I certainly would never want to miss my girls (and nieces) getting glammed up in the Castle.
If it were me, I would do Bibbidi Bobbidi Boutique before lunch, with everyone enjoying the experience, and then off to a lunch that is perfectly themed to carry the fun forward. Then, that afternoon, I would head to Pirate's League as a family, enjoy the Pirates of the Caribbean attraction and the Adventureland setting, and perhaps find a dinner that let's the boys be the stars next. A suggestion would be
'Ohana, where a jungle-like setting is ideal!
But you know your kids (and parents) best, so either strategy could work.
Have a magical experience!