Wrap pulls all of that HTML out of the page and sticks it in HTML built from the param for wrapAll and then you stick the whole bundle back on the page which means you're slapping that same script file back onto the page I assume. Any time a script tag is dropped into a page, all of its JS executes. Now I'm going to edit and make some other suggestions when I've figured wtf is going on with this app but that's your problem with the bonus firing.
Additional:
Okay, so I don't know what Smarty is. Whenever I see a Smarty-related question, something horrifying is going on so I don't even want to know. If you have any control over the app in general, you should be able to add Script tags before jQuery happens. Ideally before this tag gets appended. At the very least, add an empty function called cj before this happens to avoid the errors and then figure where the real cj is so you can plug it back in.
But regardless, if you don't have control of at least most of the HTML, get a stick and hit somebody with it until they promise to stop making horrifying technology choices and restore control of the HTML to you, the guy who is supposed to be working with the damned HTML and JavaScript to get things running.
Or show them this. I've been at this six years now. These kinds of problems should not be allowed to happen. Technology that robs us of control of our own app gets crumpled up like a paper ball and tossed over your shoulder because you will never get that time back.