The thing that isn't clear is when the voidable years were added. Originally it was a 3yr/10.5m deal, with a 5m signing bonus. Without the voidable years, his signing bonus would count for 1.66m for 3 years(2012,2013,2014). He would only "owe" for 2014, or 1.66m if he retired.
If the voidable years were there the whole time, his original signing bonus would count for 1m per year from 2012-2016 and he would owe the full 3m if he retired. But they wouldn't get it back until 2015 at the earliest and it would come in 3 yearly installments.
Either way the Cowboys shouldn't be too pressed about getting any of the signing bonus back. The signing bonus served as his salary the last 2 years and 7m for 2 years of a top backup QB is high, but not outrageous.
If he doesn't want to play at all, they should just cut him, save the 3.25m in salary and move on. If he just doesn't want to play for us, they should play hardball and fine him everything they can.