Whenever you want to change how a file starts when you open a new document you have 2 choices:
- Edit the startup files (aka New Document profiles)
- Create a template
Altering settings in these two areas ensures that all new documents begin with those settings.
In this case, you could open a startup file and re-save it with PDF compatibility set to
off. Or you could simply open a new document, and save it as a template (.ait) ensuring you disable the PDF compatibility. Then start each new document with your template rather then the
Editing startup files is fairly easy. Here is an Adobe Blog post explaining what's possible and how to edit them: http://blogs.adobe.com/adobeillustrator/2009/05/startup_profiles_a_great_tool.html
For existing documents, you would need to reopen them and then save them with PDF compatibility off. There is no default, automated way to alter the settings in unopened documents. Scripting and/or actions may be able to walk through files disabling PDF compatibility though.