My understanding was that FaceTime and iMessage weren't open sourced because of issues related to a patent troll (VirnetX IIRC). I'd be interested in hearing from others that are more familiar with the situation.
Or perhaps concern with having to deal with 3rd party iMessage/Facetime clients while at the same time trying to maintain a high level of security. Apple doesn’t want anything to tarnish the security reputation of these products.
Not only that, but apparently Steve Jobs decided to just say that on stage and while it had been discussed a bit it wasn't the plan and came as a total shock to the people involved.