This is not something that can be fixed or changed.  It is inherent to how the application works.

When a user is given a Manager or Executive persona, they get the Pipeline capability. Pipelines are created in each organization at the time that the user clicks on the "Pipeline" navigation item on the left. When the user clicks on that Pipeline navigation item, the system goes through each organization and creates a new pipeline workspace for the user in every organization that doesn't already have the pipeline workspace for the user. Starting in version 5.5 Pipeline workspace is created automatically when a user logs in with the Web client.

The pipeline workspace is necessary for the client to be able to display the pipeline page. Since personas are not organization specific, the pipeline has to exist in all organizations for this functionality to operate properly.