Instead of changing wordpress code (which has its own problems while updating), its always better to change the plugin code.
We can easily use jQuery functions as the plugin works on the “simplemodal-login” class.
So to enable it for reply comments: in the appropriate js script add the following code under SimpleModalLogin.init function:
$("a[class*=comment-reply-login]").addClass("simplemodal-login");
One can use similar logic to add simplelogin over other login plugins (instead of normal login meta link)
