Yikes. A recent virus definition update for Microsoft's free Security Essentials anti-malware software briefly had the program identifying Google Chrome as a trojan, specifically "PWS:Win32/Zbot".
According to Microsoft's virus database, Win32/Zbot is a "password-stealing trojan that monitors for visits to certain websites. It allows limited backdoor access and control and may terminate certain security-related processes."
Of course, Google hadn't slipped a trojan into its browser on the sly — it was a false positive on MSE's part. Unfortunately, MSE was fully capable of deleting Chrome without user consent, if the program's default actions were set accordingly. Otherwise, the worst it could do was block Chrome from accessing the internet.
The issue has since been rectified, with definition versions 1.113.672.0 and above vendetta-free. But, if you were unfortunate enough to get the update and find Chrome mysteriously gone moments later, then here's the why.