A couple of points:
The search head cluster is designed to allow users to directly change dashboards and other knowledge objects. Those changes are then replicated automatically to the other members of the cluster. So, what your users are doing sounds fine.
The deployer is meant for distributing baseline configurations, such as migrated settings or upgraded apps. Once the app has been deployed to the members, most future changes, such as the types of dashboard changes that you describe, occur automatically through configuration replication.
Use the deployer, not the deployment server, to distribute apps and such to the cluster members.
For more information, see the set of three topics that discuss cluster member updates, starting with this one:
http://docs.splunk.com/Documentation/Splunk/6.4.2/DistSearch/HowconfigurationworksinSHC
These sections in particular address some of your main concerns:
http://docs.splunk.com/Documentation/Splunk/6.4.2/DistSearch/HowconfigurationworksinSHC#How_configuration_changes_propagate_in_a_search_head_cluster
http://docs.splunk.com/Documentation/Splunk/6.4.2/DistSearch/PropagateSHCconfigurationchanges#The_types_of_updates_that_the_deployer_handles
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