Use elements option

[okkez]

    <script type="text/x-mathjax-config">
MathJax.Hub.Config({
  elements: ['math'],
  tex2jax: {inlineMath: [['$','$']]}
});
    </script>

This allows to convert math expression under specified elements.
We want to specify elements via Daimon::Markdown::Plugin::Math.script_tag.

[okkez]

http://docs.mathjax.org/en/latest/options/hub.html

We must specify DOM element ID's.