System is a stock wiki area. It cannot be removed by the admin, and we have not removed it at your request. I'm not sure what you're referring to. If you have manually removed it by editing the database, you have damaged your installation.
Since "System" is a hidden area (displayorder = 0), I have gone ahead and added "system" to the default value for the Auto-Link Ignore List setting in the next release. Since you already installed, you will need to add "system" manually to Options > VaultWiki: Wiki Links > Auto-Link Ignore List