The Morning Wars couldn't have happened with an organic slave species of the quarians? 
Pretty sure there's an entire franchise based on the concept. Something-something "of the Apes" 
Whether or not it could have happened isn't really the issue. The issue is how it changes the context within the story. In general, we oppose slavery, and with an organic race, whether or not they're genetically altered doesn't really matter. We consider it wrong, and that's really the end of it. Point is, the Morning War was the result of an accident. The quarians did not intend to enslave a sapient race. Doing this with organics would leave them with zero excuse. The quarians would simply be a mix between the batarians and the kaminoans. With AI's, it's trickier because there's still the question as to whether we should consider AI's alive. Even if the setting itself tries to establish that they are, the PC can still oppose this idea.