In short, I think this chart represents the character's motivations more than their actual standing in the plot. Gamagoori isn't working for a 'good' institution, but he will do anything to protect not only his sense of order, but also his sense of moral righteousness. Ryuko's revenge is only justified because she seeks to bring criminals to justice, even though she believes that these judgements must be made by her own hand.

I actually haven't thought about these alignments this way before. I play a bit of DnD, and a friend even trained me to be a Dungeon Master, but I never really had a full grasp of the alignments until now. Thank you for the conversation! Now I have a good point of reference for more analysis…