Have you tried deploying super agent to the branch sites,
Since you have a communication between main site to branch sites, you can deploy super agent to any one of the machine in the branch site that will take care of updates & policy management.
The communication between the sites is not stable.
In case that there is no connectivity between the sites, the admins on the branch site should have the ability to load updates for their site.
Is it possible to load updates to the super agent?