One allegation I run across is that the charge that the Confederates were traitors. That depends on whether you think a state has a right to secede. That, in turn, depends on your political philosophy. Are you a social contract theorist? If so, which version?
Do you take the position that an earlier generation has the moral authority to make binding choices on all future generations? That's pretty paternalistic. Surely that's rather extreme. Surely that invites many counterexamples. That's a Hobbesian view of the social contract, in contrast to a Lockean view–which grants the right of citizens to revolt.
The allegation is rather ironic considering the origins of the American republic:
When in the course of human events, it becomes necessary for one people to dissolve the political bands which have connected them with another, and to assume among the powers of the earth, the separate and equal station to which the laws of nature and of nature's God entitle them…
For that matter, is nationalism an end in itself? What's the value of a "union" if, say, a sizable majority in one region doesn't wish to belong? That's an extrinsic union which must be imposed from above. Why compel people to belong who don't wish to belong? Is that worth killing for?
Suppose a sizable majority of Alaskan or Hawaian residents voted to secede. Should we use military force to keep them part of the US? If so, why so? What's the value of coercive membership? Isn't that like empires with vassal states? Doesn't that reflect an imperialist outlook?
I suspect the allegation has less to do with an argument from principle than the specific case at hand. I think secession and states rights are valid principles. But the South squandered its moral capital by invoking those principles to legitimate an illegitimate position. That discredited the principles by association. Brought them into disrepute. The high-minded rhetoric was belied by the sordid cause.
I think the principles are still valid. But a justifiable principle doesn't ipso facto justify any particular exercise of that principle. The dilemma for the Confederate argument is its selective appeal to popular sovereignty. If that applies to Confederates, that applies to slaves. Either both "unions" are dissoluble, or neither are.
Confederate apologists could never square that circle. Either freedom for all or freedom for none.