Hi @mbmacdonald,

You can do this by setting the 'default' parameter for the course_navigation placement to 'disabled'.  For situations where you aren't using an inherited key for the tool config, this is a pretty simple addition to LTI 1.3 JSON.  In the case of inherited keys, like Lucid, things currently get more complicated.  You'd need to make this change using the API.  I do have a python script to assist in a change like this if you'd be up for trying that.  Additionally, if the inherited key is edited in the future, it may undo the manual API change, so you'd need to monitor for that and re-apply the change via API again as needed.

I have been asking Instructure to give admins more control over inherited keys, especially the default setting for course_navigation placements.  Like you, we don't want every external app under the sun to be in the course navigation by default, but we'd like to let faculty enable them if they wish.  Hopefully we see some action on this at some point.

Feel free to DM me here if you're familiar with python and need assistance with my script.

Hope this helps!

-Chris