The main thing to remember in this case is that the incident between the captain and the misbehaving gentlemen in question happened outside of the aircraft after the passengers had left it, after the doors had been opened, and on Spanish soil. Therefore, the aircraft could not be considered 'in flight' as per the Tokyo Convention. As a result, the captain in question had no immunity or special powers under that legislation and the only law applicable was the law of the land they were in. He was effectively a citizen trying to stop and ask other citizens for their identity which he had no right to.
Even though it feels wholly unfair that passengers were awarded compensation for the delay, from a legal point of view the decision makes sense.