Auto submit just a shipping method

Yes but you will have to edit the view in order to change the check on the auto submit option.
You can do that in the file shipping or payment of the view checkout via the menu Display->Views.
To activate or disable it for a view, you can change the code:
if($this->config->get('auto_submit_methods',1)){
to:
if(true){
or:
if(false){
based on whether you want to activate it or not on that view.