It depends on the defintion of taint. Homebrew cannot touch the base system, since it lives in /usr/local in macOS. Also macOS SIP prevents modification of most system files.
One major problem is that system and Homebrew versions of library may have incompatible ABIs.
That's the exact reason why I consider MacPorts much more elegant.
Most likely. I still remember the incident where I upgraded my system wide python installation manually and had to reinstall mac os