This is shifting blame to the tools. The problem lies on StackOverflow's lacking design and not in jQuery.
Pushing jQuery to the bottom of the page is trivial if you do proper HTML architecture. Pages should have only HTML. JS files only JS. JS files referenced at the very bottom of the body. Very simple. (if your asp/c#/* framework doesn't make it easy, blame the framework and not jQuery)
Inlining JS and even having JS code in the title attributes is ridiculous. Fix your HTML and only then you get the right to say anything. Another telling gem is StackOverflow page doesn't even have a proper encoding declaration.
You don't need to use jQuery for everything. This is very typical of developers coming from backend who don't take web development seriously. Use CSS as much as possible.
Another misplaced attack is refresh, with proper cache headers it should not take that long. If some browsers are slow and don't keep a pre-parsed cache, blame the browser vendor and not jQuery.
jQuery taking 80ms on mobiles is quite OK. If you really care about mobile make a page optimized for mobile and minimize JS rendering and styling.
I absolutely love StackOverflow and it's one of the best things to happen to programmers in the last few years. But this self-righteousness attack on a very important tool is very misleading and ungrateful.
Edit: the proposed "solution" of catching $.ready and later calling those is insane.