First, MathJax's internal format is MathML, so even the TeX to HTML-
CSS pipeline goes through MathML internally.
Second, the image fonts are almost never used any longer, except if
the web-fonts take too long to download, or in certain cases when
files are loaded locally from disk rather than over the web. There
are few browsers now that will require them, other than very old
versions.
Third, the MathJax web fonts are NOT based on the BaKoMa fonts in any
way. JsMath used those in its earlier versions, but they were not
very successful, and I ended up making my own fonts for jsMath v2.0
(as I recall) and above. MathJax has never used the BaKoMa fonts, and
has always used fonts created from the TeX CM fonts via mftrace and
FontForge. Unlike the jsMath Fonts, the MathJax fonts are actually
unicode fonts (the characters are in their proper locations), and that
makes them more reliable and generally more useful. They are also OTF
fonts rather than TrueType, except for the EOT fonts used by Internet
Explorer.
Davide
I will have to let others make recommendations on that, as I certainly am not an expert of that. I do know that systems like WeBWorK and Moodle allow you to create homework and quizzes, and they both have the ability to use MathJax to render the mathematics. But they might not be appropriate for your situation.
As for what you students need to download, if you use MathJax, the answer is nothing at all. There are no plugins needed, and MathJax will load the fonts it needs over the web (though it will use the STIX fonts if they are on the student's computer, which does make rendering faster).
Davide