I think the Japan comment was a legitimate attempt to expose how ridiculous its it to see an attack on an Arab city in response to an Al-Quaedi attack on America as legitimate.
unfortunately, it misses the mark. both nkorea and japan are state actors, whereas al qaeda is not a state actor and saudi arabia is. you're comparing apples and oranges: it'd be like trying to argue that it's perfectly legitimate to nuke paris because of german aggression into poland.
if you want to make an apt comparison on how illogical nuking mecca would be, this is far better: shall we nuke dublin every time a bomb goes off in belfast? should france annihialate madrid every time ETA decides to detonate a bomb in some club in Ibiza?
You can't randomly start nuking cities because of the race/religion of the people who live there just because a minority of extremists of that race/religion attack you - other wise why no nuke Japan after a N. Korean attack? Maybe 'East Asian culture' is the cause of north korea's belicosity

some problems with your position:
most people in nkorea are nkoreans. an attack by nkorea would likely be carried out by nkoreans.
the majority of people in japan are not nkorean.
if you really want to get that deep into it, tell a japanese that he's korean at heart. no, even better, tell a korean he's the same race as a japanese person.
ON THE OTHER HAND:
it seems as if a sizeable fraction, perahps even a majority, of the people in al qaeda self-identify as muslims and saudi arabians. the few attacks perpetrated by al qaeda in the us have been dominated by saudi arabian muslims.
the majority of people in mecca are saudi arabian and muslim.
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