You don't say so, but I guess you are using either Django or Jinja2 templates on the server side. In which case, no they wouldn't ignore content inside a mustache script tag: for one thing, they know nothing about mustache, and secondly it's fairly common practice to actually put server-side template tags inside Javascript, for instance to provide initial values for functions.
In Django versions greater than 1.5, you can wrap your mustache tags with the {% verbatim %}...{% endverbatim %}
tag to prevent server-side evaluation. Jinja2's equivalent is {% raw %}...{% endraw %}
.