One, this article and the project it covers will be good negotiating leverage against Microsoft's fee increases. I wouldn't be surprised if they end up winning back lower license fees and sticking with MS in the long run.
Two, what a boneheaded move on Microsoft's part, PR-wise. CERN is an internationally-respected research institution which is widely admired by the kinds of people who make purchasing decisions. Why poke the bear, especially when business is going so well?