Pardon my ignorance, but if those exceptions are possible then doesn't that make Bitcoin just another manipulatable fiat currency? As it matures, influence will pool into groups large enough to execute exceptions after their own interests.
I think you'd have to do this in two stages. First, create a version of the client that accepts a particular exceptional transaction if it appears in the blockchain. Wait for a supermajority of clients to switch to the new version; once the fraction gets high enough, everyone else will be forced to upgrade too, or risk being on the losing side of a schism. Then it would be safe for miners to actually execute the transaction.
As the owner of 51% hashing power, you can try to convince the network to update by holding it hostage and threatening a DOS attack by mining without verifying transactions, but I don't think that would be economical either.