Those commie hippies Ben and Jerry -- Blackwater can dip them head first into a melted cauldron of Cherry Garcia and Chunky Monkey.  Oh wait, they don't own the company any longer.

Illegitimi non carborundum.

The Civil War was a morally and legally complicated situation.  As thefadd pointed out, seceding was one thing and firing on Fort Sumpter was another - although some historians have claimed that the attack on Fort Sumpter was just a pretext for a war that was going to happen anyway, and that the attack might even have been faked by the North.  

But aside from that, there was the issue of slavery.  Slavery was, of course, enshrined in the original US constitution, so you couldn't legally go to war about it, yet slavery was morally indefensible and had to be stopped, at virtually any cost.  I would personally say that the moral imperative to end slavery was greater than the moral imperative to respect the constitutionally guaranteed rights of the southern, slave-holding states.  You could then point out, if you wanted to, that the North went to war to prevent the South from seceding, not to end slavery.  The end of slavery was actually just a military strategy. Lincoln wanted to be motivate the slaves to desert their masters and to join the forces of the North.  Slaves were better motivated to do that, knowing that they would not just wind up as slaves again when the war was over.  This gave them something important to fight for.  It was a clever strategy.  Nonetheless, the practical consequence of the Civil War was to end slavery, and therefore it must be considered a morally justified war.  So in that sense, I would say no, the Confederacy did not have a right to secede.  If the slaves are granted no rights, then I equally well deny that the slave owners have rights.  What's good for the goose is good for the gander.  If you don't believe in human rights, then you don't have any.

If we did not have the issue of slavery to deal with, I personally would have believed that the Southern states, who had joined the United States voluntarily, also had the voluntary right to withdraw.  I also believe that the basic principles of democracy would very much support the right of any group of people to make their own decision about which political entity they would want to belong to or would not want to belong to.  Democracy, ultimately, is about giving people the kind of government that they want, rather than forcing upon them the kind of government that they don't want.  It is about governing with the consent of the people.  If the people do not consent, then the government loses its democratic legitimacy.  

So in general, I believe that any section of any larger political entity should have the right to secede if it wants to.  There probably should be some minimum size requirement.  (I would speculate that a population of at least 50,000 is reasonable to qualify for independence.)  It would be ridiculous if, let us say, a family of four decides to secede and form their own country.  If that were acceptable, then we might as well give up on government entirely, and declare a general anarchy.  I would also say that if the human race manages to become more socially advanced, then anarchy does become an attractive option.  With no governments, it would never be necessary for anybody to secede, since there would be nothing to secede from.

Confederate states had the right to secede. They didn't have the right to fire on Fort Sumter. The South's many and myriad strategic miscues are well documented, the valor of Robert E. Lee notwithstanding.

make it rain you nappy headed ho's

    I would argue that the Southern states had no right to unilaterally secede, though any state probably could via constitutional amendment-- if a majority of the rest of the nation no longer wants you, perhaps it's best for everyone if there's a split. (There's also the possibility that a majority of states could, essentially, expel one or more states via this process, though "division" would be a better word than "secession" in that case.) The argument that this makes it easy to enter the Union but hard to leave doesn't sway me much; most legal contracts are easy to enter, but hard to exit, unless the circumstances are agreed upon beforehand. Not the case then, nor in the case of Vermont today.
    War, OTOH, is its own justification. A nation founded on armed rebellion as a colony can't- or at least shouldn't- ignore the reality of violence as a means of self determination. Whoever wins is "right", as has been the case throughout history, IMO. Machiavelli saw this clear enough, and the fact he was labeled "a most evil man" for centuries shows how much kings, presidents, and intellectuals like to avoid or obscure where state power really comes from. ("Death is the coin of the realm for the state", as Robert Anton Wilson puts it bluntly.) It isn't very pretty, and certainly not consistent, but IMHO that's the way it is.
    I'm not as far out as to follow Crowley's Rights Of Man to the letter, but it's a lot closer than many other thinkers I've read.

Ex ignorantia ad sapientiam; e luce ad tenebras