At this point of development, GooTool is stable and can be used safely without much concern. GooTool left "beta" status on just before its first birthday in October 2009.
GooTool does not modify your original game installation. It asks you for a place to save your "custom" World of Goo, which is a copy of the original plus any addins that you have installed.
Be assured that GooTool does not, and will never, have viruses. All releases are built on Linux and are virus-scanned before being published on this site.