I have very mixed feelings about homebrew. When it works, it is awesome, but when it doesn't it can be a serious nightmare. In particular, homebrew refuses to run under sudo. Instead, to instal in /usr/local it wants me to recursively chown /usr/local to myself, which is a Really Bad Idea (tm). I have mostly stopped using it for this reason. I understand that running a program that runs third-party scripts under sudo…
If you're concerned about safety, you could maybe "freeze" your homebrew install by chowning /usr/local back to root in between brew invocations.