Here's an idea, create a Handlebars helper, that will compile handlebars.
With this sample, I believe you can build something that will suit your needs:
<script type="text/javascript" src="http://builds.handlebarsjs.com.s3.amazonaws.com/handlebars.min-latest.js"></script>
<script>
  var data = [{
    "title": "Hey",
    "subtitle": "I'm an inner handlebar template.",
    "html": '<h1>{{title}}</h1><h2>{{subtitle}}</h2>'
  }, {
    "title": "Nice!",
    "html": '<h1>{{title}}</h1>'
  }];
  
  /** Handlebar helper that will compile the content passed, with the data at index **/
  Handlebars.registerHelper("compile", function(content, index) {
    var template = Handlebars.compile(content);
    return template(data[index]);
  });
  var content = '{{#each .}}\
    {{{compile html @index}}}\
  {{/each}}';
  var template = Handlebars.compile(content);
  
  document.body.innerHTML = template(data);
</script>
 
 
I never used ember, but I believe you can make it work easily ;)