After graduation, we have a better-matching font. I am still not completely happy with the current state.
I looked how much effort it would be to make \ce
fit better to the surrounding text, like $\ce{H2O}$. This posting is to whet your appetite.
Before:

After:

How you can try it out yourself:
- Open a page in Chrome, e.g. https://chemistry.stackexchange.com/q/45190/24052
- Open Dev Tools (Chrome on Win: press F12)
- Go to Sources tab
- Open cdn.sstatic.net/Sites/chemistry/all.css
Paste the following two lines
.MathJax span.mi[style="font-family: MathJax_Main;"] { font-family: inherit !important; font-size:90.09%; }
div.MathJax_Display .MathJax span.mi[style="font-family: MathJax_Main;"] { font-size:100%; }

This sets all upright letters with the font of the text body. Numbers still have the TeX font – which is not 100% matching – because the body font has old style figures. Inline TeX is set to 100% font-size to match the surrounding text, while display-mode TeX stays with 111%.
This his is just a prove of concept. It applies to one MathJax renderer only, namely HTML-CSS. It is a hack and for a proper solution, a MathJax change would probably be needed. A lot of things are missing (text in subscripts, etc.), but I think this gives a good impression of what could be possible.
Does this whet your attpetite? Then we should go forward talking to the MathJax and the SE developers. Otherwise, just state so.