Hi David—
If you have to use a non-Arbortext conversion process, then you will probably have to convert Arbortext’s math markup to something else you can render in the browser. The first thing I’d try is converting the Arbortext math markup to MathML and then use MathJax to handle rendering in the browser.
If you can make that work, it might be worth the effort to do a one-time conversion of all your documents to replace the Arbortext math markup with MathML, and then maintain it that way going forward. That would open up a wider variety of tools to you for editing and publishing the math expressions. (MathFlow, Design Science’s MathML editing and publishing system, has a nice API you should be able to integrate with your publishing pipeline independent of Arbortext.)
Another approach would be to convert the Arbortext markup to (La)TeX, and then use a TeX engine to convert the expressions to graphics in a parallel process using something like TeX4ht.
--Clay