Try it using javascript.
With using a framework like jQuery its easy so find such tags inside a frame or popup window. You can try it by something like this:
var allATags = $('myFrameId').find('a');
$(allATags).each(function(index, element){
var href = $(element).attr('href');
//here you shall try to find out if there a mailto Link or a normal link, e.g. using regular expression or indexOf()
[...]
if (isMailToLink){
//split the href String at the signs '&' with which the subject, mail, etc is splitted and removing the mailto, putting all in own variables
[...]
$(element).attr('href', 'javascript:void(0);');
$(element).click(function(){
showMyMailForm(toMail, mailSubject, mailBody);
});
}
});
On opening a document in a frame or a popup wait for the document being loaded and then run your code to replace all existing mailto-links on that document with your mailform-mailer.
The code is just a way trying to inspire, no working code.