Hi,
This is Peter from the MathJax team. It would be extremely cool of Disqus added some support (back -- people had found nice workaround before disqus switched to iframes).
Our documentation might be a bit unusual because it's really for uninformed users and content authors not so much for developers; we admittedly carry a bit of baggage after 6 years of development, too (e.g., we still semi-officially support IE down to 6).
Anyway, MathJax is very modular with various input and output options. Szabolcs seem to refer to TeX input which is one of three ways to input mathematics (TeX, asciimath, MathML); there are also three different ways to output it (HTML/CSS, SVG or MathML). Each input also comes with a separate pre-processor, so you can use whatever delimiters you like ($...$ for TeX are actually no the default though most TeX/LaTeX users like them).
I think it comes down to how much control you want to have as Disqus vs control you want to give site-owners. (Not saying you have to give them any.) An opt-in for site-owners seems most sensible (allowing some customizations like input/output choice, delimiters etc; compare to existing Wordpress/Discourse/etc plugins maybe). You'll probably want to enforce the safe extension
http://docs.mathjax.org/en/latest/safe-mode.html to get some sanitization.
Regards,
Peter.