Majora =/= FD mask, I don't even think Link could safely wear Majora's Mask, and he has a pure heart.
This would be easier if we knew more about Majora. I always viewed it as influencing it's wearers to act upon their darkest impulses while giving them the power to do so. I think Majora has no end goals apart from causing as much chaos and destruction as possible. So how much would it's influence do to Ganondorf? He's already evil and he has power of his own. He's not out for revenge like Skull Kid was, he's out to find the Triforce, so I doubt it would make him drop a moon on Hyrule.
But really, Ganondorf wouldn't be bothered with Majora's Mask because he's focused on the Triforce to get power.