ACF cannot do this by itself.
There is this, but I don’t know if it will work for your purposes, I haven’t tried it: http://support.advancedcustomfields.com/forums/topic/new-addon-for-multisites/
If that doesn’t work then the best choice would be to use a standard select field rather than a relationship field. Then you can dynamically populate the select field. http://www.advancedcustomfields.com/resources/dynamically-populate-a-select-fields-choices/
