In the case of the Civil War, as I have said, logic was on the side of the Confederacy. If a state could voluntarily join the union, then it should have had the right to secede from the Union.
Morally, slavery was immoral and wrong. Also a bit hypocritical, since the nation had agreed to end the importation of slaves, but still allowed for their purchase and sale within the boundaries of the country. It was illogical to say that slavery was moral and the basis of the economy in half the country and immoral and curse to the country in the other half.
Politically, the South pushed the Northerners with the Dred Scott decision and the fugitive slave laws too far.
The poor Whites who did most of the dying were the suckers, since they had absolutely nothing to gain and everything to lose. Samuel Clemens, aka Mark Twain, had the proper solution for a young man from a slave state: leave it all behind and light out for the territories. When surrounded by insanity, one should always do one's best to flee.
Al Qaeda is not really concerned with internal American politics. They simply want to return the Muslim countries to some idealized XIV century caliphate, which is far more unrealistic that Reagan's and now the teabaggers' desire to return to the "good old days" of the 1950's. I agree that Al Qaeda is in a state of war with the US, and therefore membership in Al Qaeda makes them subject to the rules of war rather than the rules of civil law. I don't see where American citizenship is much of an issue if one joins a terrorist organization pledged to kill Americans.