MTed: "Sic semper" was indeed a rallying cry! Sic semper tyrannis ("Thus [shall it] ever be to tyrants") is the state motto of Virginia... hence the line in the song about Virginia not calling out that particular refrain in vain, when she meets her sister states on the "plain" (of battle), as they "baffle" (impede the movement of, thwart, ruin) the "minions" (servile dependents of a powerful force [abolitionist sympathizers, presumably, since this was written in 1861] ) back "amain" (forcefully or violently).

All that's missing is the rain in Spain...

But seriously, "Sic semper tyrannis" was supposedly what Brutus said when he and his co-conspirators assassinated Julius Caesar. Guess who was inspired by this story of tyrannicide? John Wilkes Booth! Here's an excerpt from Booth's last diary entry (April 26, 1865):

"with every man's hand against me, I am here in despair. And why? For doing what Brutus was honored for. What made [William] Tell a hero? And yet I, for striking down a greater tyrant than they ever knew, am looked upon as a common cutthroat. My action was purer than either of theirs. One hoped to be great himself. The other had not only his country's but his own, wrongs to avenge. I hoped for no gain. I knew no private wrong. I struck for my country and that alone."

As Uncle Dave O says, the propaganda that equated states' rights with the perceived "right" to enslave other human beings (who were portrayed in song and in other ways as being of an "inferior" race), and that equated abolitionists with tyrants, certainly pervaded antebellum and Civil War-era Southern society. This propaganda was certainly evidenced through popular songs of the era that decried "tyranny".

How curious that the Confederate song "We Conquer or Die" contains a description of "the stern bigot Northman".