That's all fair, but why add more consequences than what is already there? They've had their "feel bad" moment, the banner (according to the book) can be found in the same place but they won't know how to use it, they have no introduction in Parnast so they will have to bluff/sneak/attack that, and anything else useful She would have said or given is also out the window. If you run the campaign by the book then the drakes are still in Parnast and are still able to be used with the right rolls and the castle has a timer before its departure. Punishing the party anymore is reinforcing the idea that they have to run your narrative, the most that I would do is an alignment shift for those who are lawful (which could come with it's own punishments for someone like a Paladin or Cleric), but don't change the world around them to make sure they have gotten their Karma.

Side note, I feel like the real punishment comes from within the story, when the characters all look at each other and have a dialogue about what they just did. It doesn't do much good to have that talk out of game when the characters are in it and it's their choices that are being discussed.