From one of my earlier replies, I pointed out that just like BSD, you cannot uninstall Cydia, only reinstall. You can, however, go into terminal, and run the following command to remove the GUI (and keep the subsystem):

apt-get remove cydia

You will then be asked to confirm by responding with: Yes, do as I say!

When thats done, restart springboard, and you will be Cydia-less again, but still with the awesome subsystem that it comes with. If you ever feel like installing Cydia again, you can either Reinstall it from Installer, or you can do:

apt-get update
apt-get install cydia