We have very little control over this. Physics Stack Exchange is part of a network of 160+ sites. All the sites share a common engine, so it is possible to request and obtain site-specific changes to the common behaviour, but they need to be very well justified.
The place to request changes to the engine is at the overarching meta site, Meta Stack Exchange, where it is easier to get the attention of the community team and the developers. Our meta site is better for issues specific to this site and its community.
Frankly, I don't think it's particularly problematic. The entry-level badges are awarded easily as an incentive for new users to explore the site's features, by adding some fake internet sugar on top. In the grand scheme of things, though, it's not that important.
On the MathJax side, though, you're right, but that's not quite the right approach - I advocated this one earlier
but it's not yet implemented and it just went live.