С помощью eval и регулярных выражений
<div id="test"></div>
<script>
window.onload = function () {
var txt = "Hi-<script>alert('HI!'); <" + "/script>hi \
Ha-<script>alert('HA!'); <" + "/script>ha";
test.innerHTML = txt.replace(/<script>(.*?)<\/script>/ig, function (a, b) {
eval(b);
return a;
});
}
</script>