There are two routes: Use either rbenv or RVM. There are recipes for both below. Before you do, you probably want to turn off the installation of local documents for gems.
echo "gem: --no-ri --no-rdoc" >> ~/.gemrc
Then:
run:
rbenv install 2.1.2 (or whatever version you prefer)
rbenv global 2.1.2
gem update --system
This installs an up-to-date version of the gem system in your local directories. That means you don't interfere with the system configuration. If you're asking this question, you shouldn't be messing with system security, and you'll spend longer understanding what issues you may run into, than just having an easy way to avoid the problem you started with. Learn InfoSec later, when you know more about the operating system and programming.
For an alternative use 'RVM' instead: To install rvm run:
rvm install 2.1.2
rvm use 2.1.2
gem update --system
This has the same result, you end up with a local Ruby and Gem system that doesn't interfere with the system versions. There is no need for Homebrew, or over-riding system libs, etc.