To your last paragraph, yes, I agree that the south was not attempting to rule America. Hence, it is improper to call it the American Civil War. England, Russia, and China had legitimate civil wars, for example.
Now, you can't blame Lincoln for southerners being of inferior intelligence to Americans. The "oh, he tricked them into attacking Sumter" line isn't even an argument. The CSA should have had the sense not to attack a greater power, and the decency not to seize what did not rightfully belong to them. Period. The north did not hold majority rule in government for much of the 19th Century up to that point. When the south left, they did so with their own man still in the white house. I blame the south more for 400k dead American troops than for slavery.
Finally, you are either an American patriot or you are not. If so, then you hold American values above those of the English crown and the Confederacy. The three nations cannot all be viewed as equally worthy of one's devotion to a true patriot.
This idea of 'patriot' muddies the waters. Is there anything between 'patriot' and 'traitor'? The founding fathers for years said they didn't want to declare independence, but only to have England not act as badly as it was - eventually they decided England wouldn't do that. Can a government ever mistreat its citizens, much less it colonies, enough that they're justified in seceding and it's not an issue that they're not 'patriots'? Once they seceded- of course it was an issue for the north to keep forts in the south.