So it seems Skype had a deal with Prism before MS took them over.
They where also not the only one to hand over info. Yagoo, Apple, and Google also forked over info.
In a quote from MS.
We do not provide any government with direct access to emails or instant messages. Like all providers of communication services, we are sometimes obligated to comply with lawful demands from governments to turn over content for specific accounts, pursuant to a search warrant or court order.”
So it boils down to the government making them hand over the info. It was not them freely offering it to them.