All it took for Kakashi to dispose of the gas masks was a flick of his finger. Since he was the creator, he had the final right of destroying his creation.
Just as they stepped out of the washrooms, he flicked his finger and made the gas masks disappear.
Everybody took off their face masks and dumped them in their pockets. It was Reon's advice– since shit could get out of hand if the Scientists report an attack (which they would report) and face masks from their side are found here (which would not happen).
Then Kyoryu proposed the only two options they had– Lair or Academy. Atama had called them anyway, and Hitori wanted to meet Akemi, too. So they all decided on going to the Academy.