He's the most public face of the company. He made his political/religious/moralistic political stand, now he has to suffer the scrutiny, like anybody else in his position.
He's failing to lead the company as a result of this stand, and trying to keep quiet about it now that the horse is out of the barn.
He gambled that people with his view would remain in the majority and that there would not be serious repercussions and a calling out for an explanation at some later point.
He was wrong, so now he's got all this scrutiny, which is what happens to CEO's.
The same sex marriage issue didn't turn out the way a lot of religious people thought it would as years went by, they thought that their religious views, and imposing them upon other churches and other religious people would somehow not come back to bit them in the ass. They love to make the issue out as being about some sort of PC police thing, and play the poor victimized Christian martyr. The reality is that other Christians and their churches have been and are just as much in disagreement with them. They tried to wield a power and authority that hurt people and their families and now they're crying about it. It's too bad, but they deserve the reactions they are getting now. If they'd shown a little compassion and deference and respect early ont hey wouldn't be in the position they've created for themselves.
They deserve it.