I have given this some thought as well! Link definitely has that "enemies closer" viewpoint, and he is very curious/suspicious (though not quite ill-meaning) toward Ganondorf at this point and would not be against joining a crew with him. The only real IC drawback is that his absolute allegiance is to Hylia. I think it really depends on what sort of a conclusion they come to together, especially since it's likely that Link will mention Ganondorf to her.