Currently there is no feature in Q2A to hide pages. Deselecting the page in options only hides the menu item. It is something that has been suggested before though so there may be more control in the future.
However you can remove the page with a core hack. The file for the home page is qa-include/pages/default.php but that also contains stuff for categories and custom pages. Look for this comment:
// If we got this far, it's a good old-fashioned Q&A listing page
Then you'll need to add this line:
return include QA_INCLUDE_DIR . 'qa-page-not-found.php';
If you want to block the /qa page and the default category pages (example.com/categoryname) put that line above the comment. To block /qa only, put that line inside the next "else" clause after that comment, around line 137 like this:
} else {
return include QA_INCLUDE_DIR . 'qa-page-not-found.php';
$sometitle = qa_lang_html('main/recent_qs_as_title');
$nonetitle = qa_lang_html('main/no_questions_found');
}
That will make a 404 page on the "recent questions and answers" page.