The problem is, as you say, we have no solid proof. We don't even have endgame savefiles to view.
AFAIK the only thing that gets send to the MV servers is the endgame XML, possibly with some additional info about the savegame. That means that not even Stardock may have access to the games themselves.
So that leaves us with these possibilities:
Stardock say 'in dubio pro reo' and the scores stay. Without proof, this seems likely, however suspicious these games are.
Stardock say 'these scores - in comparison to other expert scores - are proof enough' and bans the accounts.
Now, the only proof we could have is if either of those two come forward and provide a savegame or at least describe their strategy in detail. Highly unlikely. On the other hand, I'd bet there are enough coders on this board that in a concentrated effort, we could try to arrive at the same result, thus proving to Stardock how these cheats work. That, however, could get ourselves into trouble.
It would be nice to know if these scores are actually under investigation, though. Kind of like in Formula One, where there are those messages saying that a certain incident is being investigated by the stewards.