Sure, but I don't think many people at Microsoft have security clearance to begin with. Like when the NSA reached out to some middle management Joe on the Outlook.com team, he/she probably did not have security clearance.

Entire groups of people at MS have clearances. Their software runs large chunks of the DOD, they can and do put consultants on site in secured locations when needed. Who else is going to fix an exchange cluster that has been mis-configured by a lowest bidder tech?

Many of these (all?) companies have CISO or CSO executives, who's job it is to handle these specific things.