thanks for your question!
I'll answer in English, so that everybody can benefit from this. If you have trouble understanding, please send me an email, and we can continue in German then. (The address is in the main plugin file "tablepress.php".)
I don't actually recommend putting the TablePress Default CSS into your theme's style.css, for several reasons: After an update of TablePress, you might have to manually update the CSS again, and you take away the opportunity to easily update your theme (unless it's a custom or child theme anyway).
Of course, it is still possible to not load the TablePress Default CSS. To do that, please
1. Revert that change in the controller-frontend.php! You should not modify plugin files directly, as you will lose those changes after a plugin update.
2. Instead, just add this line to your theme's functions.php (or create a small plugin around it):
add_filter( 'tablepress_use_default_css', '__return_false' );
And yes, new tables will automatically have the "Use DataTables" checkbox checked. Fortunately, this can also be changed with a small piece of code. Please see http://tablepress.org/extensions/datatables-off-new-tables/ for more information, and just install the small TablePress Extension from there as a regular plugin.