The argument in these posts is basically that libertarians shouldn't sympathize with the Confederacy, because the Confederacy did not pursue libertarian policies.
This statement is, of course, true – to some extent. The flip side of the statement is also true – libertarians shouldn't sympathize with the Union because the Union did not pursue libertarian policies.
Libertarians who are concerned with ideological purity should be against both sides. After all, war is the health of the state.
I would argue that the people in the war who deserve the most sympathy from those who love peace and who love non-authoritarian, non-centralized government were a segment of the Confederate troops. For the reasons why, let's turn to Charles Francis Adams (who fought for the Union and whose liberal credentials are unassailable) – from my review of his essay:
Then Adams tries to make a distinction between Virginia's decision to secede and other Cotton States' decisions to secede. The latter states seceded when Lincoln won the election. Virginia did not. Virginia believed in secession (as did everyone who ratified the Constitution, according to Mr Adams). Virginia was willing to let the other states peacefully secede, but did not wish to secede with them. Only after the US government tried to re-supply Sumter, an act of war against a sovereign state (i.e. South Carolina), according to the logic of Virginia and the original understanding of the Constitution, did Virginia rebel. According to Virginia, the North had effectively changed the Constitution at that point and Virginia seceded to defend the original Constitution. Mr Adams understands this argument but sees it as hopeless outdated and out-of-touch. Nevertheless, he sees it as consistent. Lee then went with his state.
The Civil War was a disaster of epic proportions. The North freed the slaves, but left the slaves in a condition often worse than slavery for the next several decades. The net result for the "former" slaves was hardly a significant improvement. On the other side, government chosen by the people was dead. There is no way to argue that Southerners have agreed to live under the Constitution. The State expanded like never before. Even the idea of limited government was shot – as Lincoln ignored the Supreme Court at will. There is little here for libertarians to sympathize with.
The South of course was, in large part, fighting for slavery. However there were some in the South – as Adams was intelligent enough to note even though he fought a war against the same men (I wonder why today's commentors can't view the war with the same level of detachment?) – who fought for their idea of limited, freely chosen government. To the extent that libertarians should sympathize with any men fighting at that time, I would pick these few, proud men.