With Fury (comics) or Steve (movie) in charge, the white command structure would be preserved. And since the entire division was captured, it was not only possible, but historically accurate, that regiments within the division could begin as segregated.

Of course, during the capture and escape, everyone would have gotten jumbled - as they did in battle historically -.and a special, commando team could get formed from the survivors.

I'd also like to point out, in view of a fic that had Gabe being formally listed as white to preserve the illusion of segregation,
that Jim would have to be handled as well; and with his last name, it would have been nowhere near as simple.