I'm going to go out on a limb here and assume you're really talking about using a Javascript framework (JQuery, Prototype, Moo, etc) and not necessarily AJAX. The problem probably isn't that your HTML is in here docs but more than likely the HTML is pretty loose and not well structured.

If you have well structured HTML, injecting JS to make the page more 2.0ish will be a breeze ... it's just that 'here docs' are a big *red flag* that your HTML is probably a mess and will need to be re-written to conform to the more demanding requirements of a JS framework. Template toolkit is not necessarily going to give you that structure either - you can write crappy HTML in template toolkit as well.