The way i read what you wrote the students were suspended for wearing T_shirts that were anti gay and not because of there biblical content unless there were other students wearing tshirts with non religious anti-homo statements who werent suspended. Therefore the is not really a case for civil liberties. If they didnt support the day all they needed to do was not wear the cards and talk in the hallways. If they were suspended for that then would have a case for a civil liberties group.
Of course i dont know much about the ACLU so I am basing my opinion on the facts as presented in your post.