Unlike voice, video calls is a real minefield. Think about how long voice calls have been around. Most of the patents for voice calls are on the compression algorithms. Most of the video call patents are for the act of making the video call.
And they could open source it and leave it to the community to handle licensing but you'll eventually end up with fragmentation as some clients implement features that others won't.
If others own the patents, Apple can still open Facetime with the requirement the anybody who wants to use it has to go to the patent holders before it can be made into a product.