Well, by just stripping out the script tags and document.write stuff - I can make it work perfectly with JS on, but the graceful degrading to noscript when JS is off is lost. When I comment out the noscript tag, everything kind of turns out okay, but I'm sure there's a more elegant solution. It does still work with JS off, though (the pop-up, not lightbox).

Here's my hack of /includes/modules/YOUR_TEMPLATE/additional_images.php -- line 91

Code:
    // Link Preparation:
	// begin zen lightbox v1.2 aclarke 2006-09-07
    $script_link = '<a href="' . $products_image_large . '" rel="lightbox[gallery]" title="' . $products_name . '">' . $thumb_slashes . '<br />' . TEXT_CLICK_TO_ENLARGE . '</a>';
	// end zen lightbox v1.2 aclarke 2006-09-07

   // $noscript_link = '<noscript>' . ($flag_display_large ? '<a href="' . zen_href_link(FILENAME_POPUP_IMAGE_ADDITIONAL, 'pID=' . $_GET['products_id'] . '&pic=' . $i . '&products_image_large_additional=' . $products_image_large) . '" target="_blank">' . $thumb_regular . '<br />' . TEXT_CLICK_TO_ENLARGE . '</a>' : $thumb_regular ) . '</noscript>';
It doesn't degrade as gracefully, but works for now. I'm guessing the code could use some escaping to fix it.

Thanks for the add-on! I look forward to the compression and stripping of the JS to a smaller filesize.