There's currently a grand total of 3 games (or titles at least - one is a compilation) by I-Magic/iEntertainment on GOG and none have been added for a while but I was looking at their back catalogue of stuff that ISN'T here and they've apparently got titles called
American Civil War: From Sumter to Appomattox
North vs. South: The Great American Civil War
Don't know how good they are but they'd probably be theoretically easier for GOG to get hold of than anything Take2 controls, if GOG had the will that is...

Other than that, for stuff actually ON GOG, Colonization and Conquest of the New World don't quite hit the mark but they're the right continent at least!

Maybe I'll mention Expeditions: Conquistador even though its South and not North America too...

Oop and now a Mobygames category:
http://www.mobygames.com/game-group/historical-conflict-american-civil-war/offset,0/so,1d/

There's also a new ACW game in development, Ultimate General: Gettysburg, designed by the creator of the well-known DarthMod series for the Total War games:

http://www.ultimategeneral.com/

Not sure if there's any hope for getting this game to GOG.com, but won't hurt to vote for it:

http://www.gog.com/wishlist/games/ultimate_general_gettysburg