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.
That's always been the case; however, it is only manipulable via consensus, rather than by a centralized command structure (one CPU, one vote). There is already a great deal of the concern about the centralization of mining pools; two or three of the largest pools could currently collaborate and hijack the block-chain (although theoretically, it's not in their best interest to do so).
Currently, if you control 51% of the network hashing power, then you can force the longest branch of the blockchain to contain anything you want. However, another client's view of the blockchain will reflect the longest legal branch that it sees, by its own definition of legality. Any miners that don't consider it to be legal will start their own fork. (This is exactly what happened, briefly, with the LevelDB fiasco some time ago.)
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.
You'd still have to convince most users and stakeholders of Bitcoin (merchants, exchanges, etc) to update to the new version in order to avoid a Blockchain fork, where both sides of the fork are likely to lose and the currency is destroyed.
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.
