I think you'd agree that "[MathML] is designed as a presentation markup language" at least needs qualifying, given the content/semantics part of MathML and Mathematica's authors' substantial involvement in its development.
To anyone looking at adding MathML support to an editor like Sigil, I'd first suggest having a look at http://www.w3.org/Math/Software/ to see what the options are. There are a few approaches one could take for an initial implementation, from using human-editable ASCII representations à la TeX for simple uses (mentioning x² and the like in body text) to launching an external application for more complex uses. The external application might even be something that can only export to MathML rather than editing the MathML directly (so long as Sigil keeps track of what the input file is). Granted, these simple approaches are nothing if not "unoptimized"; but they're a start, and using TeX-like input is no worse than what academics have been doing for a few decades.