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!

I think the idea is that a wargame is more like D&D, and less like the Olympics. It requires cooperation to keep the illusion intact, so there's a limit to how "sweaty" you can be trying to win. After a certain point, you're exploiting the limitations of the scenario rather than the weaknesses of your opponent.