This sort of malware spreading often hides itself from (a) logged in users and be (b) browser strgins that aren't Google. This can ultimately hurt your Googlerank if for no other reason than serving a different page to Googlebot than you would to outsiders. And yes, Google checks. This is why they used to have a campaign to register your mobile site with them if you were sniffing for mobile useragents.
It's not good. Change your user-agent to googlebot (User Agent Switcher is a good addon for Firefox.)
I accidentally still had it on from trying to read an article that some site was showing exclusively to the googlebot but paywalling for everyone else. If I hadn't, I wouldn't have noticed.
See http://www.mattcutts.com/blog/fetch-as-googlebot-tool-hacked...