What if Bashir is only working for Section 31 not because he necessarily thinks it's right, but because of a combination of general pragmatism and given that it's totally within S31's rights to exploit the Augments under Federation law, he wants out of the Institute and is the only one of the group stable enough to do so? He "got volunteered", as it were, and has finally gotten enough resources - or fed up enough - to make a clean break away from S31 for his freedom?