There are definitely problems with homebrew, but user-owned directories isn’t high on the list, imo. Your ssh private keys, startup scripts, and any number of other things that can do serious damage are all owned by your user. Frankly, if install vim as my user, I want it to execute instead of the built-in version, unless I’m running a command with sudo, in which case the system binaries take precedence. So I don’t even see path order as a major issue here. If someone has compromised your user, you’re compromised whether you’ve used homebrew or not.