Courses and course formats

You don't mention which Moodle version, so that _might_ make a difference to answer.

However, a quick look at the code suggests this is something that really shouldn't be able to happen for a site admin, unless you are trying to delete the 'front page' course for the site (usually id=1). If you are logged in as the site administrator, then the capability check for being able to delete the course should automatically pass (indeed, as site admin, all capability checks are hard-coded to pass).