The recently released version 2.1 of MathJax should allow you to do the same arrangement with MathPlayer and MathJax with MathML output. You should be able to update your copy of MathJax to v2.1 without having to update any of the rest of WeBWorK, if you want.
I realize that this is still suboptimal, and there are some alternative approaches that are under development to allow MathJax to improve accessibility in browsers other than IE.
WeBWorK Main Forum
Direct MathML
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