Small font size seems the easiest to fix. Kerning seems worse since people will manually tweak spacing with \, etc, so you can't just change it whenever you want.
For example, a\mathbin{foo}b is supposed to render as "a foo b", but on GitHub it comes out as "afoob".
When I looked at the MathJax configuration GitHub uses, nothing pops out as being odd. It would be funny if a minifier totally messed up the part of the MathJax source code specifically for this.
However, even if it's theoretically possible to change the font size, would Github ever do so? My impression is that as an organization they place a high value on interface stability. Very little about how I interact with the site has ever changed.
I suppose that individual publishers might stick in a hack to increase the font size, but a bad default means that as a consumer, I'll be stuck looking at tiny math on Github for the vast majority of documents.
GitHub tunes the UI all the time.