I don't think it is proper that the Mono Framework installs a /usr/bin/pkg-config symlink. It is misleading, and as this is a Mono-specific pkg-config, it doesn't scan /usr/lib/pkgconfig (which Apple mysteriously provides even if they don't provide a pkg-config) anyway.
A configure script for some random software might see this pkg-config and think that the system provides pkg-config in the "normal" way and try to use it to get information about MacOSX system libs, and then fail. (If there was no such bogus /usr/bin/pkg-config, that configure script hopefully would realize that it needs to use other methods to find out cflags and libs.)
This is not just a hypothetical example, but happens when building LibreOffice. The configure script in some of the 3rd-party libraries bundled with it get confused by this /usr/bin/pkg-config.
This also causes breakages in https://trac.macports.org/ticket/25318 and a number of homebrew things.
/usr/bin is owned by Apple. /usr/local is also in users' $PATH by default, and is a more appropriate place for user-installed crap.
See also this post from debian regarding PKG_CONFIG_LIBDIR: http://lists.debian.org/debian-embedded/2004/06/msg00122.html
I have deleted the /usr/bin/pkg-config symlink from my system. If you want a patch to make this less broken, I will provide, but I don't want to try to fix it until I know why it was broken.
What is it that you are trying to achieve by breaking pkg-config anyway? Avoiding known-broken versions of packages on the system? (You can do that by specifying your package versions more precicely.). Maybe I should dig through the revision history to find out who to shout at.
Following up on what David said, I'd like to see this resolved in Mono as well. Installing a Mono-specific pkg-config anywhere in the standard PATH is a bad idea, as it's likely to be picked up by general builds. Since it's already otherwise nicely sequestered in the Mono framework, it's really not necessary to create the symlink in the first place.
Has there been any progress or followup for this issue? I reencountered this problem today when a Homebrew user encountered a build error that we eventually tracked down to this: https://github.com/mxcl/homebrew/issues/16050
This is fixed in https://github.com/mono/bockbuild/commit/73b43b83c38f72f1c9fdc9099974eceef038df0c