Yes. He had to because Apple threatened to ban him if he did not comply. Since he was a small indie dev, he couldn't exactly create a twitter/media firestorm and get away with it.
I once saw an iOS app hit by this same IAP shakedown quite recently. The developer, a friend of mine, had called me in an emergency to help expand his backend for Apple payments. It almost felt like a protection racket run by your friendly neighborhood Mobster.
The most egregious thing is that they don't inform you about this beforehand, event when they could easily stop this on the first review. They will let you on the store, get users, and then sneak up on you and hang your users over your head to get you to comply.
I really hope dhh sticks to his guns and starts up a revolution against Apple.