Either you are incorrect, or this functionality is non-obvious. Based on recent experience, I'm leaning toward the former.
When I go to edit my blocking options when a site doesn't play nice with Ghostery, I'm given options either to disable certain tracker-blocking or to disable Ghostery entirely on a given domain. There doesn't seem to be an option to stop blocking a given tracker only when its loaded from a certain site.
There is one tracker I've unblocked because it breaks functionality on one site, and I'm fairly certain I've seen its effects on a different site recently as well. It doesn't seem to have unblocked that tracker only for the one site I need it disabled to use.