https://github.com/facelessuser/BracketHighlighter
And is it crazy overall, or just when it comes to handling brackets from a plugin, in which case, it might just be a corner case that was not originally catered for?
Highlight colors should be the responsibility of highlight themes, and users should be able to change them by changing the theme they use or adjusting it to their taste, not by ...hacking into a plugin that hardcodes them.
At best you could argue that the plugin could be allowed to hardcode a color, and themes could optionally override it -- but even that breaks separation of concerns.
Even if it was crazy (which it is not) it's a tiny part of ST (just how the syntax highlighting works), and wouldn't be proof of any general "crazy architecture" of the editor.