It makes things safer, but not 100% safe. In the June hack the hacker deliberately crashed the price to .01 to try to transfer more coins out. I don't know if it worked.
If someone roots the server they might be able to circumvent the transfer limits. There are more possible levels of protection - they might store the wallet on another machine that only processes transaction batches, verifies that there are no excessive withdraws, and doesn't have any other communication with the outside world. That's how I'd do it, but I can't say if Gox does.