The CSS Alabama was a Confederate warship know for it's proclivity for sinking New England ships. It, n turn was sunk by the USS Kearsarge. The song commemorates this final action and would not have been looked kindly upon in the South, had they a clue about the history.

This reminds me of a friend who served with the USAF Pipe Band back in the 60s. While somewher below the Mason-Dixon line, they were asked, "Can y'all play a Southern tune?"
Whereapon the band struck up "Marching Through Georgia." No one got it.