Reading this, I was actually surprised to find that for some reason or other this has gotten a lot better for me during the 2+ years I've been using uMatrix.
At first it's rather annoying to enable CDNs and stuff for the sites you frequent, but mostly I've started noticing that the sites that break for basically no good reason are the ones that a sane person probably shouldn't visit anyway. So maybe it is just that I've started steering clear of those sites.
Also as a side note, uMatrix is awesome. Many times even on HN I'm surprised to find comments complaining about pop ups or something, and realize that uMatrix silently made my browsing actually tolerable.