That may be so, but your FAQ didn't even exist until after Flashback broke out, if the document history doesn't lie. So my comment stands.
Well, to be completely fair, the FAQ did indeed exist before the news officially broke about FlashBack having been found to infect Macs. (It was actually created in August 6, 2011. About 6 weeks or so before Intego
announced FlashBack's existence on September 26, 2011.)
You can view the changes to the FAQ here. I have found the comparison where the recommendation to disable Java was first added to it, somewhere between 2-3 weeks before news officially broke about FlashBack having infected Macs.
http://guides.macrumors.com/index.php?title=Mac_Virus%2FMalware_FAQ&diff=22953&oldid=22648
Now, FlashBack was known to exist prior to this. In fact, going back to as early as Fall 2011. However, at that time, there were no published/verified reports of any Macs being infected. At least, none that I have found within my searching.
But, what I find kinda funny about all of this, is that FlashBack is a trojan bundled with a modified copy of Adobe's Flash Player. It's not related to Java in any way that I know of, unless I'm missing something (that's possible ... wouldn't be the first time.)
... and now, to the OP's post!
Keep an AV and anti-malware product on your Windows system (I use NOD32 and Malwarebytes AntiMalware Premium). Keep them up-to-date, and be diligent with their scanning. That's about all you can do there, short of stop using TeamViewer altogether, that is (which is probably not an acceptable solution.)
BTW, your friend should "practice safe browsing" too, if their system is expected to be the source of malicious code. If the concern is really
that serious, though, I would simply stop connecting to their system altogether, but that might not be something that you are prepared to do for whatever reason.