Hi Kai.
Well, I'd just comment out original code in qa-page.php and then add necessary code in head_script() function within my own theme.
But if you want to get complete upgradeability, I think, you should parse $this->content['script'] within head_script() function override before calling parent::head_script() and unset jQuery's entry (I think, code like false!==strpos('qa-content/jquery',$scriptItem) would be enough to detect necessary entry). It's a rather bad thing in fact, but it looks like Gideon didn't left us anything better. There should be no html rendering in the core at all, but, alas, it's not the case...