All it takes is one wrong person to be assigned as a report comes in, a person who doesn't understand the real value of a bounty program, or one person having a bad day to completely ruin a company's reputation. It seems like that might have happened here (of course MS has done this before so who knows if it'll matter in the end).
Microsoft needs to be completely transparent and to do so immediately. They should, with the reporters permission, release all communications. They can exclude technical details if patches aren't available yet. Doing anything less is going to prevent a lot of people from using their bounty program in the future and we'll all be worse off for it. They almost certainly made a mistake and they need to own up to it.