I think, I just talked myself through the solution. Forget both of those scenerios where we have to link and unlink. However, we still want to create the custom fact "Public Trees"
Now we create a shortcut in the FTM media folder to the URL of the family tree regardless of the site.
We create a new source for the "Jones Family Tree" and add the existing media (the shortcut) to the media tab of the source.
Now, just setup new links to the individuals contained in the Jnes family tree you are interested in. No having to go back and unlink all those bogus facts.
So tract the tree your family members are in, setup a quick link to the tree and avoid merging all together. The only compramise, I have to make is still setting up a Public Tree as a "Source" vs. being handled as a lead, which would have been my first choice. Of course there are no accomodations for leads anyway.
I suppose any of the procedure will accomplish the same thing. Just a matter of how much manual setup and entry you're willing to do.