I think the problem with that lies with how the Ajax IM stands right now. Very unnoticeable when you receive a new message from someone (if you have no chat tabs open). And when people add messages back to you via the IM after you've closed your chat with them and left the site, you wouldn't know about it until they're online again and you open the chat with them. That's why it'd be a good idea to fuse the messaging system.
Also, Private Messages are good for sending offline messages, so if the two messaging systems are fused Private Messages would need to be kept in order to hold functionality for sending messages to your offline friend.
While I'm at it, I also want to say it'd be a nice idea to have the friends you talk to the most always be listed on the Chat List, online or offline so it could further promote the functionality of one chat system.