This isn't the issue from last fall, but Apple addressed questions regarding FaceTime security from ZDNet. An Apple representative assured the site that the FaceTime conversation stream is encrypted from end to end, specifically with WPA2 Enterprise encryption. Each FaceTime session has unique session keys for each conversation.
What this does is make FaceTime HIPAA complaint as long as the wireless network being used utilizes WPA2 Enterprise security with 128-bit AES