Ajaxify WordPress Site(AWS) Issue

I’m using Ajaxify WordPress plugin, which is working great, but if I include any script tags within a page linking to a file <script src=””></script> its is removing the tag and stopping other pluggins or theme javascript from working.

I can see you’re removing all scripts here

// Fetch the scripts
					$scripts = $dataBody.find('#document-script');
					if ( $scripts.length ) $scripts.detach();

and adding again here

// Add the scripts
					$scripts.each(function(){
						var $script = $(this),
							scriptText = $script.html(),
							scriptNode = document.createElement('script');
							console.log(scriptText);
						try {
							// doesn't work on ie...
							scriptNode.appendChild(document.createTextNode(scriptText));
							contentNode.appendChild(scriptNode);
						} catch(e) {
							// IE has funky script nodes
							scriptNode.text = scriptText;
							contentNode.appendChild(scriptNode);
						}
						if($(this).attr('src') != null) {
							scriptNode.setAttribute('src', ($(this).attr('src')));
						}
					});

Any ideas?