Wow, it's almost like people do crazy things when overcome by grief and anger.The siege of Theramore lasted days before the Horde forces withdrew, under combined assault by Alliance Forces and Kalecgos, giving the civilians plenty of time to escape before the bomb was sent and blew up the port and the military forces that stayed behind.The civilian refugees were later captured and taken to Orgrimmar where they were caged as prisoners of war until the Siege of Orgrimmar when they were released by the Horde and Alliance forces as they secured the city level. The civilians were not treated kindly, but they also weren't slaughtered, even by Garrosh "I'm Totally a Hitler Allegory" Hellscream.
Jaina planned to flood Orgrimmar and drown every single orc, innocent or otherwise, in her grief over losing Rhonin and Theramore.
That you don't see the difference, there, is kind of chilling.