I've run into this same situation and have figured out how to use the API to change the default state. A point of clarification-- this will disable the link in the course navigation for all courses by default (not just new courses) as long as the link hasn't been used in the current course.
This took me awhile to figure out, so I hope this will give you a head start. You can run the following code in PowerShell:
Invoke-RestMethod 'https://YOURINSTANCEHERE.com/api/v1/accounts/1/external_tools/TOOLIDHERE/course_navigation[default]=... -Method Put
You'll need to update your instance url, tool ID (newly added to the LTI report in Canvas), and generate an access token.
As an additional note, any time you make an update to the LTI, the course navigation seems to default back to enabled. I hope this helps. 😀
(Sorry the code above wants to default to a link.)