What is the significaance of the metaphor O'Brien uses to describe Jimmy Cross's reaction to seeing his soliders search for Kiowa's body?

I think the metaphor you are referring to might be,

"The filth seemed to erase identities, transforming the men into identical copies of a single soldier, which was exactly how Jimmy Cross had been trained to treat them, as interchangeable units of command. "

Even though each soldier had different identities, the army trained him to see them as one nameless unit to get the job done.