What should have been done (as was done with German and Italian Americans): nothing
German- and Italian-American social organizations, even utterly inoffensive-seeming ones like the Sons of Italy, were placed under heavy wartime surveillance, even though practically none of their leaders were actually arrested or interned. I would have supported the same kind and degree of surveillance for Japanese-American organizations, combined with the additional protection from mob assaults that Ferguson97 mentions. No internment, no arrests except on probable cause for specific individuals, no outright bans on the organizations being surveilled.