Evidently, Japan is a lot more tolerant than most nations.  Flying into or over a nation's airspace can be considered an act of aggression, and it would be perfectly alright to deal with it appropriately.  I would hope any violation of our airspace would result in the offending aircraft's being shot down.  I think Japan should so warn North Korea, and then act on it next time.  It seems the path of most North-Korean missiles is over Japan.  By cutting off that route, the Japanese would be doing the entire world a favor.  And if Japan needs help from an ally--say, the U.S.--I'm sure that ally would be happy to assist.