Yeah, the interesting thing is that we know exactly how Lovecraft himself would write this scenario: it's Chapter 2 of "The Call of Cthulhu," complete with sinister swamp mulattoes and everything. The fun of this scenario is going to lie mostly in subverting that form into a totally different type of horror.
You guys are thinking in the exact same direction I am. The PCs are going to be escaped slaves. I'm probably going to set this in the 1850's instead of during the Civil War proper. I think there won't be any white characters in the entire scenario, except some terrifying slave catchers and probably a few cultists -- nothing brings people together quite like Cthulhu!
Like most of the Civil War scenarios, I'm looking to design it as a one-shot, though the whole setting could easily be a campaign seed.