2) Bitcoin Foundation could setup some public servers that always run the latest official version of the bitcoin client. Exchanges should then be able to verify that the transaction is legitimate
I guess any self-respecting exchange is already running their own instance of the latest bitcoind for that purpose.
But MtGox is not a self-respecting exchange, that is the problem.
The funny bit is.. they keep sending transactions with spend inputs! Right now! With withdrawals blocked and problem, as you claim, being identified.