I haven't had time to go through enough questions to make up my mind on whether I'm OK with this aspect of the new design or whether I think we should go full blast and change to a serif font, but I do want to note that the problem is at least much better than it used to be - and give credit to the design team for addressing this.
Compare the same example I used in the original request, with the new fonts vs the old ones.
###New CSS
###Old CSS
In the old fonts, the LaTeX tends to stick out like a sore thumb, but it definitely blends in a lot better with the new ones. I'm holding judgement on whether it's enough or not for the moment, though.
###Added:
And indeed, things are not quite there yet, particularly with comments: consider for example
seen here, and obviously suffering from Sore Thumb syndrome. (Running chrome v48 over ubuntu, MathJax 2.6 with local STIX fonts, in case it's needed. It would be good to hear from others whether it displays this badly in other systems.)
Similarly, for that same comment, it appears that Firefox (v41 over Windows 7, MathJax 2.6 using web TEX fonts) produces this horrifying sight:
