I don't believe there is any release or deployment process for userJS on the projects, certainly nothing formal or standardized.  In some way, Gadgets 2.0/3.0 was designed with these issues in mind, but that project is currently stalled, as far as I know.  What you're doing is likely what I and other WMF folks would recommend (version control, tests if feasible, careful deployment with an announcement to users if you have some channel of communication, etc).  If you'd ever like a quick security review of the code or possibly some aggregated data on its usage, feel free to create a task in Phabricator.