There is no explanation or justification for any of the requests in this issue.
The typical system administrator, to urgently recover from a problem, will need to use local system commands to disable plugins indicated a problem in the Jenkins logs.
The first step is to include a "README" in the install and/or plugin directories. This readme file may be as simple as to link to the Jenkins online documentation describing the file structure and configurations.
Not sure what's needed here, but please note that the Jenkins folder structure is mostly considered to be opaque to users and messing with it without knowing really well what you're doing will generally not work (such as the issues users who bypass the plugin manager and use chef to manage plugin while ignoring dependencies experience). Adding this README would elevate messing with Jenkins home to a "supported" use, which it is not.
Secondly, there should be clear documentation on the "manual" backup/restore/disabling plugins and their configurations.
There is, linked in your comment.
Lastly, if it is not currently possible to disable a plugin via the command line and/or config update a process should be added to Jenkins to do so.
(Correction: The UI broke as it's the auth plugin – JENKINS-27175 – but it's documented on the wiki, and easy enough to understand how $JENKINS_HOME/plugins works.)