Frankly MSN messenger as a tool inside business communication has failed. Microsoft wants to push that Live Server (or whatever it's called), so purchasing most used 3rd party VOIP system inside businesses is quite logical.
I don't know what IP Skype possessed, but if they have some dumb patent on VOIP technologies, Microsoft's legal machinery will use that. I'd fear that more than canceling Linux port. Besides, it's not too far fetched to expect Microsoft developing Silverlight-based Skype client, which would mean a native version for us too.