This is also a reason why you shouldn't run installs as root if you have a choice either: use something like fakeroot, then mv into place (possibly repeating anything with systemwide effect the package did, like ldconfig). This is annoying, but necessary :( (doubly necessary with some core packages, like glibc, where if you do a raw 'make install' of a working glibc you are quite likely to end up with an unusable system!)
Not that using a package manager necessarily saves you. An old Solaris bug springs to mind, which thankfully never bit me:
4137237 patchadd 106300-01 results in rm -rf / as root