So far there's been no official word on passenger car paint schemes, but I expect that, other than replacing the VRE logo with an Army one and VIRGINIA RAILWAY EXPRESS on the side with U.S. ARMY, they won't get too extravagant because this costs money. If the Army wants to use the cars as rolling billboards for recruitment purposes, perhaps a flashier paint scheme will appear, but don't expect camouflage because these aren't tactical vehicles.
As for which costs more (security vs. repair), it depends upon whose pocket it's coming out of. I don't know if VRE is responsible for delivering the cars intact to the Army or if this simply wasn't considered in the contract and it's left up to the Army to foot the bill, but if it involved leaving the cars for any length of time in an unsecured area (and that was a given), it certainly should have been included in the contract. It's a simple fact of life - if you leave things out, people will steal them. I well recall a drill sergeant in basic training warning us that "Your buddy will f*** you, Joe! Your buddy will f*** you! He'll steal your d*** if you put it down!" And he was right, too.