I started releasing all premium themes that I created for Q2A as free products under MIT license. I used a simple method to add Theme Options to admin menu and a web form containing options including even reading custom files and loading list of images used for background patterns.
the method is pretty simple:
1. create a file with layer class as in it, I use "qa-admin-options.php" file name.
2. add content of your form in $this->content['form'] inside doctype() function.
3. add a navigation item with link to your Theme Options url in nav_list() function.
4. use this code in top of you qa-theme.php file to load the layer you created.
$theme_dir = dirname( __FILE__ ) . '/';
qa_register_layer('/qa-admin-options.php', 'Theme Options', $theme_dir , $theme_url );
to make sure that normal users can't access theme options simply check logged in User's Level on doctype function, so both viewing and processing form submissions from None Admins will be rejected.
for more information check one of my themes on github with theme options, for example Esteem Theme.