As others have noted, OS X comes with various open source packages pre-installed. While this can be a nice convenience, the packages often are only updated to new versions as part of a major OS X release (like 10.5 to 10.6). Also, some packages are used elsewhere by other parts of OS X and there is no easy way to know which. In general, Apple assumes (and you should, too) that everything under /System/Library and /usr/, except for /usr/local/, is part of OS X and is administered by Apple. You should not attempt to remove or modify files in those hierarchies. That includes just about all of the open source packages, including Ruby.
Instead, to upgrade an existing package, the right approach is to install a new version in a separate location (say, /usr/local/) and invoke the new version by an absolute path reference (/usr/local/bin/ruby) or manipulating the shell PATH environment variable, if necessary. /usr/local/ is often used if installing directly from source. Many people prefer to use one of the 3rd-party open source package distributors, such as MacPorts, Fink, or Homebrew, each of which has its own package manager and installation locations.