Currently in Creo 2.0 there is no method to disable auto check in. At out company, we have found that the auto check in can be problematic since the user does not get a chance to review what is being checked into Windchill. Also, there is no comment box to document what has changed. We would like to have the ability to either disable auto check in or change the default behavior to use the custom check in.
In the meantime, we are adding the custom check in button to the Quick Access Toolbar and recommending that our users use it to check in objects.