I wouldn't mind in the least if it was a matter of using sudo. That's a logical elevation of privileges. MacOS already does this at points, asking you for your password (which if you are an administrator is basically running sudo for you). These warning messages and locking down the /usr hierarchy (even with sudo) are different as they aren't asking for more access but merely to spread FUD about open access software (yes, you can use brew if the program you want is in it, but that is just adding another garden even if less walled, and it works because someone in the Homebrew project is signing the binaries).

I have used UNIX/Linux on a daily basis for over 30 years, and OSX/MacOS daily for over 15 years. I know how UNIX systems work and where things traditionally are located. And until a few years ago MacOS was a reasonable UNIX that could be used more or less like a friendly UNIX system -- but it is becoming increasingly less so.