While creating the ETL template, the query timeout is fixed.
What you can do it use a query which finishes in less time (by limiting the number of rows using a timestamp filter in the query). This will make sure that the ETL template is created successfully and can be consumed from creation of ETL.
While creating the ETL from the template, you can use the actual query which you want to execute.
Hope this helps. Let me know if you have any further query.