Games for Windows Director Kevin Unangst has confirmed the status of Age of Empires in a post on Gamerscore Blog:

"As many of you have heard, Ensemble Studios will be closing after Halo Wars is complete. If you're a PC gamer, you've likely played some version of Age of Empires somewhere along the line. I want to reassure you that Microsoft will still own the Age of Empires intellectual property. As a company, we're very excited about the future potential for Age of Empires, and as a PC gamer I'm looking forward to what that future holds. Stay tuned."