if your filter and Mathjax plugin for Atto are the ones in Jason's GIT I accidently found them yesterday and tested right away (and checked also what you have done with CKEditor and TinyMCE4...)
There is a long history behind different editor plugins and math renderers - have you read any of those discussions? Simplifying things is good but using accessibility as a reason to strip more advanced tools may not be the only way to go.
Have you considered fallbacks - if something like java or flash does not work in all mobiles, tablets or screen readers you can give different, more accessable tools for those devices or hide not-accessable tools in such devices.
I comment here shortly the latest mysterious statements (opinions?) in http://docs.moodle.org/dev/Editor_2.7 about Equation Editor
- CKEditor: Has mathjax plugin - uses different maths delimiters so needs hacking to make it backwards compatible with our existing equations.
- Atto: Has mathjax plugin - requires newly written mathjax filter but is 100% compatible with existing equations
- TinyMCE4 & 3.5: Has dragmath plugin. Java based - ugly, not-accessible.
Math renderers, filters and editor plugins are 3 separate things. MathJax is a math renderer script that can be used to render different types of math output: a small subset of LaTex http://docs.mathjax.org/en/latest/tex.html#supported-latex-commands with some custom commands but also MathML, SVG, AsciiMathML output formats,... The code that math renderers output on pages of moodle can be accessible even if the tools that were used to create the notations were not.
MathJax can use several delimiters so it is not a problem if old notations used double dollars and new plugins use some other delimiters (CKEditor plugin) - no need to hack the plugin, just add the new delimiters to configuration of MathJax. On the other hand double dollars are not "reserved" for old tex filter syntax.
If a site has used tex filter with some distribution of LaTeX or TeX , let's say core Mimetex or TexLive, you can't claim that MathJax plugin of Atto is100% compatible with existing equations. It's simply not. There is no universal Latex - different distributions of Latex can render different kinds of things with different extensions and MathJax can render parts of those things + MathJax has many new features that old renderers did not have.
About "ugliness" of Dragmath or Java - it's your opinion, right?
You need to give these tools settings to allow site users select what and how they want to use their tools, not to suppose that all users need simlar tools with similar settings.