I don't think it's an intentional reference, but Nagisa's look there reminds me exactly of how older Ruri (from the Prince of Darkness movie) looked. Funny how parallels sometimes happen even accidentally or subconsciously, Ruri was a child prodigy as well who was part of a team who tried to stop/save someone on the good side who went dark after losing their most important person who was put out of their reach to form part of a super system and wow are there more parallels then I thought of between those movies until I wrote this very post. Obviously entirely different in every other way too, but some themes are pretty eternal I guess!