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 ;)