I'm not so much accusing the game of being inherently harmful - the issue with a root kit is that you have ZERO control over it. If it crashes - your whole computer crashes because you can't end the task. If the software they run gets compromised - you have NO way to protect yourself. Your system becomes the bitch of whoever uses a future vulnerability.
Yeah, that's really it. A rootkit isn't necessarily malicious, but it's not safe. It's like buying a new console and Microsoft requiring that you give them keys to your house so they can make sure you don't cheat.