Maybe this is easier with the way homebrew does things (I prefer MacPorts) but then you have to manage a bunch of symlinks to bring in the stuff you DO want to use by default.
I actually hadn't thought to try this approach, though. The next time this happens I will definitely give it a shot.
(Though I use those as daily-driver packages on Macs and have actually never had something break? GNU tools tend to support BSD options.)