I suspect that they wouldn't be that stupid. That would alienate sizable parts of the Skype userbase. Microsoft is stupid, but not that stupid. This seems like pure paranoia to me.
The reason to buy skype is for it's name, not for it's tech, as everybody agrees it's tech is not worth $8B. The name is only important if it gets you something. It will get you phone sales if you're the only one offering it on a phone.
Now, what's more likely, is the way Google handles it's Maps, Nav, etc: It's available for iPhone but it's way better on Android.