I would imagine, lore-wise that the dead Khajiit were probably lynched by some stuck-up Stormcloaks. Khajiit aren't in a sense 'weak' in Skyrim, I'd just say outnumbered and unloved. Though I do have tremendous respect for Ysolda for being at least one open-minded Nord in the province who isn't ashamed of it.
Although, to avenge my people I typically raid Stormcloak camps and murder everyone, leaving the Captain alive, only to have Kharjo put his brains on the war map with his mace. As I have convinced my fellow Khajiit friend to help me in my secret Crusade to administer vengeance to those who pick on the Khajiit for no good reason.