This is totally crazy... BUT... I have workaround. I signed up for Yandex and created my own and experienced the same mess that you were going through - something in LimeSurvey is creating a mess out of the JavaScript that Yandex provides. Some of the things that I unsuccessfully tried included turning OFF the XSS filter, putting the script in the description, inside a question, etc. Nothing that I tried from the front-end works.
My workaround is to create a new PHP file (mine is located at .../application/unc/yandex.php) then do an include in the .../application/helpers/common_helper.php at about line 7839. I added the line with "Yii::import('application.unc.yandex.php');" just before the return of the function.
function getFooter()
{
global $embedded;
if ( !$embedded )
{
Yii::import('application.unc.yandex.php');
return "\n\n\t</body>\n</html>\n";
}
global $embedded_footerfunc;
if ( function_exists( $embedded_footerfunc ) )
return $embedded_footerfunc();
}