Some of what you're saying is fair. The simulation did have known issues, including glitches with point-defense systems and ships being placed unrealistically close to Red assets due to peacetime constraints on the exercise. The Wikipedia article on MC2002 acknowledges these shortfalls directly.

But you're presenting very specific technical claims (that the boats couldn't physically carry the missiles, that the fleet was "teleported" next to the armada, that the defense simulator was "turned off") as though they're established fact. None of that appears in any sourced material I can find. If you have sources for those claims beyond "interviews from other MC2002 participants," I'd genuinely like to see them.

More importantly, you're glossing over the part that actually matters: what happened after the restart. Red Force was ordered to turn on their anti-aircraft radar so it could be destroyed. They were forbidden from shooting down approaching aircraft during an airborne assault. They were told to reveal the location of their own units. The JFCOM's own postmortem report stated that "the OPFOR free-play was eventually constrained to the point where the end state was scripted."

Even if you accept that the initial result was partly an artifact of simulation quirks, the response wasn't "let's fix the sim and rerun it fairly." It was "let's force a Blue victory and use that to validate the concepts we were supposed to be testing." Van Riper's complaint wasn't just that he won and they took it away. It was that a $250 million exercise was turned into a rubber stamp.

Your chess analogy would be more accurate if, after your opponent crashed the server, the tournament organizers restarted the game but told you which pieces you were allowed to move, then published the result as proof their strategy was sound.