If the commissioner determines that probable receipts for the general fund will be less than anticipated, and that the amount available for the remainder of the biennium will be less than needed, the commissioner shall, with the approval of the governor, and after consulting the Legislative Advisory Commission, reduce the amount in the budget reserve account as needed to balance expenditures with revenue.
You might want to read the entire statute, as well the briefs submitted by both sides before relying on the news media (who do not have law degrees, mind you) to properly interpret a legal ruling. Documents can be found here: http://www.mncourts.gov/district/2/?page=3775.
It looks like the Commissioner and Governor did exactly what they were supposed to do in the event of a budget overage.