The difference is that we don't know what went on behind the scenes. Was the joke made after an agreement to not single Jada out? This joke was not part of dress rehearsal so it easnt sanctioned by the Oscar production staff.
The difference, as you pointed out was that one bald head was by choice, the other was not. Baldness is not a style choice for women. Its usually pretty devastating; about the only thing more devastating (bodily) is a mastectomy.
The difference is that Chris Rock has a history of going after and mocking black women in particular. Not that long ago he apologized to black women and promised to do better. Now this.
The difference is that there is a difference between a joke and mocking someone. His joke on the Arsenio Hall shoe may have been poorly delivered, but he wasn't mocking the guy for being bald, he was joking about having to wax one's head to maintain it's (by choice) baldness.
I'm not defending Will Smith. He fucked up. Response shouldn't be disproportionate to what happened though. He's not evil. Most of the vitriol he's getting is not about what actually happened, but about the different set of rules for people of wealth vs the rest of us.