So why did the Blue Team lose the Millennium Challenge? Where were its destroyer-equivalents? Were they deliberately excluded from a massive $250M free-play wargame for operational reasons? If so, why wasn't Ripper explicitly told that this type of attack was out of scope?

Ripper's tactics probably did have a perfect destroyer-equivalent counter. The entire question is: why didn't the Blue Team bring it? You can't declare yourself victorious because a counter to their counter theoretically exists - you have to actually preemptively include it in your forces!