When you get the "Positions Reported on the ... statement don't match those in your Money account" pop-up,
Always select
"No, do not update my account. I will make any necessary changes myself."
This will prevent the bogus RemoveShares transactions from being generated.
Set up Money Sunset to keep a lot of backups. If you make a mistake and generate a lot of bogus RemoveShares transactions, you can restore a backup to undo that. Or just delete the unwanted transactions.
I don't think a scrubber could be made to save you from this workaround chore.