Peter: This sort of configuration may work well for our needs because Drupal puts a class of "html" on <body>. I can wrap any of the selected MathJax areas with a "tex2jax" class. I am definitely open if you know of some better way, but this will do.
MathJax.Hub.Config({
extensions: ["tex2jax.js"],
jax: ["input/TeX","output/HTML-CSS"],
tex2jax: {
inlineMath: [ ['$','$'], ['\\(','\\)'] ],
processEscapes: true,
processClass: "tex2jax",
ignoreClass: "html"
},
showProcessingMessages: false,
messageStyle: "none"
});