I’m using the following instructions for using a CI model outside of CI:
http://codeigniter.com/wiki/Calling_CI_models_from_outside_script/

I tried it in a little test script and it works fine.
However when I use with an URI containing blablabla?id=123

I get the error:
The URI you submitted has disallowed characters.

I can prevent this by allowing = and ?  ( set in config file ) but, then I get the error:
404 Page Not Found

It seems that the Wiki suggested approach still causes some parsing of the URI.
Can I avoid this?

I simply just would love to have access to all libraries, helpers, models and config values without having to be under the control of a controller.

I hope you’ll find help in the user guide. In fact CI doesn’t work with the GET queries.
I don’t know well Calling_CI_models_from_outside_script, but I made this other way to use CI from external apps. The one I made will remember the GET query while in CI and reconstruct it back when coming back to your external app.
Maybe you could give it a try, or try to tweak Calling_CI_models_from_outside_script for it to play well with the GET array.