It's the same problem Dropbox had a while back. Apps using the Dropbox SDK (including the main Dropbox app) showed an interface where you could log into your Dropbox account or click a button to let you sign up for one. Since Dropbox has some paid account plans (like GitHub), Apple decided that this functionality violated its rule stating that all spending that takes place inside the app must happen using the In-App Purchase API so that Apple can get its 30%.

Apple wants devs to use in-app purchase to sell things in apps . If you don't they don't get their 30% cut of all sales. It's the same reason Amazon can't sell books in the Kindle app, they have to direct users to the website.

I think what ocscardelben meant was that Apple wouldn't get any commission off of new, paid, GitHub accounts.

Since GitHub charges based on a monthly subscription, you can't have an app that charges for a service without going though Apple's In-App Purchase program.