For those that do not want to wait for an official version, I made a short GreaseMonkey script that will hide sites you specify. Use this page to get the official names to use when setting the "ignore" variable. Multiple sites should be separated by a comma (,) and it works best if you avoid putting more than 1 space after commas.
// @name Hide SE site from Hot Questions
// @namespace stackexchange
// @description Hide certain Stack Exchange sites from the Hot Network Questions list.
// @include *stackoverflow.com*
// @include *superuser.com*
// @include *serverfault.com*
// @include *askubuntu.com*
// @include *stackapps.com*
// @include *mathoverflow.com*
// @include *.stackexchange.com*
// @version 1
// @grant none
For list of Stack Exchange sites, look here:
Put your excluded sites here under variable 'ignore'. Example, if you want to ignore Arqade and Mathematica:
//This is just an example list, I have nothing against these sites, they just happened to have Hot Questions when this was made
var ignore="Programming Puzzles & Code Golf, TeX - LaTeX";
This should work in all major browsers, but I only tested in Firefox. If you have questions, leave a comment. If you have improvements feel free to edit the answer.