You can catch the link onClick, call pause to the Youtube control and continue with opening the link. More like this:
Remove the href from your link, and set a #mark. Set an id (let's suppose is myLink). Catch the click on the link:
$("#myLink").click(function(e) {
//call pause on your Youtube control. See this response: http://stackoverflow.com/a/12522499/335905
// as long as you are not calling e.preventDefault(), the link should continue opening as expected.
});