Why would these men attack fellow southerners?

The men demand to know where the group is headed, and if they’re “with the rebels.” They will kill anyone, even fellow Sotherners, if they are rebels.

Aslan forgot to mention the fact that they were Nuer Rebels and most of the people in the group were Dinka, Jur-chol, and some other tribes. Plus Dinka and Nuer are rivals so that's another reason why they killed Salva's uncle.