Hi Daniel,
You should be looking at Eclipse Oomph which can help you automate the installation and setup of your workspace. You can add the SonarLint plug-in as a requirement, list all your projects in a project set to be automatically checked out from source control, and adapt the configuration files as required, etc.
We have added org.sonarlint.eclipse.core.prefs to source control with the reference to the project and module on Sonar. The Sonar server is also pre-defined.
The only manual process left is for our end users to generate their token on the Sonar server and enter it once in Eclipse.
Philippe