/usr/obj is left around so you can do partial upgrades(something you should know exactly what you are doing when attempted), and/or rebuild the kernel without having to go through a buildworld again. The updating instructions for FreeBSD recommend you manually delete this directory prior to an upgrade to avoid any possible troubles with only binaries being left around in the build dir.
# make buildworld
(or any other target) then the source tree doesn't get touched. That's also the beauty of this (in my opinion) because for security reasons (unwanted tampering) I keep /usr/src mounted read-only all the time. So even during the build process. # svn update
.