Homebrew (unlike Macports) does not put programs ahead of system's
General convention is in fact to put /usr/local/bin ahead of /usr/bin.  This is doable via editing the /etc/path file or sudo launchctl config user path "/usr/local/bin:$PATH".  This will cause executables in /usr/bin to be shadowed by the ones in /usr/local/bin.  The Homebrew FAQ suggests this. 

Homebrew recipes will deliberately not link any programs into /usr/local/bin that could potentially cause system-wide conflicts (homebrew executables are actually installed in /usr/local/Cellar and symlinked to /usr/local/bin).  When you install a potentially conflict-causing package, homebrew will warn you about it, and say something to the effect of "We didn't automatically link this package.  If you really want to, you can run `brew link ..." Homebrew is generally pretty good about being respectful of existing system packages.

As an empirical anecdote, I have always shadowed /usr/bin with /usr/local/bin and have never run into any issues.  YMMV, of course.