In the account reports, you could run an enrollments provisioning report for the current term to see what courses users are enrolled in.  If you have multiple active terms that you want to keep users from, you could run the report multiple times.  You could then use that data to see what users from a users provisioning report are not actively enrolled in a current course.

If you are planning on using SIS imports to make the changes you may want to use the SIS Export reports for enrollments and users instead so that it is already in the format needed for an SIS Import.

How do I view reports for an account? 

Canvas Default Account Reports