Regarding hiding the Integration Mappings field in Rally if there is any impact it might not get picked up by the API when the Clarity Integration Mapping Job is executed.
Release : 16.0.1
Rally team confirmed permissions in Rally are managed at the Project level.
So, if a user has editor rights to the Project, they will be able to edit the Integration Mappings field values.
Given that the Integration Mappings field is only for integration management purposes, and isn't needed in the UI, you could make the field hidden.
This means that people wouldn't see it in the UI (which would reduce the potential for people to update), though they could update via the API if they have the editor permissions.
However, Rally is looking at providing more granular security and we would recommend submit a request as a Rally enhancement to address this need for more granular security.