Just add delegate: 'a' to your jquery function and make sure the img tag contains the full res image while the href contains the thumbnail.

$('.popupgallery').magnificPopup({ 
    type: 'image', 
    delegate: 'a', 
    closeOnContentClick: true, 
    image: { 
        verticalFit: false 
    } 
}); 

$('.external-media').click(function( event ) {
    event.preventDefault();
    var items = [];
    $.ajax({
            url: jQuery(this).attr('href'),
            type:'GET',
            success: function(data){
                $(data).find('.slide').each(function() {
                    items.push({
                        src: $(this).attr("src"),
                        title: $(this).attr("alt")
                    });
                });
            },
            complete: function() {
              $.magnificPopup.open({
                items: items,
                type: 'image',
                gallery: { enabled: true }
            });
         }
    });    
});