I'm not familiar with the billing issues mentioned in the article, but it seems to me that Rovio is just trying to leverage themselves into an advantageous position in the market. There is big money in being a payment system provider as has been shown by Apple and Valve.
It could be very easy for them to force their way in the door too since they will be using the carriers to accept payment. This could give them huge support from cell carriers since they will be recieving a cut as opposed to the iTunes Store where Apple keeps 100% of the profits.