Without a doubt this will be used as propaganda against the entire Open Source community. Everything OSS.
I'd bet the Sales & Marketing Dept. at Microsoft and the all the rest will have talking points in their sales peoples hands before the end of the day.
At this moment, there is nothing about this on the Filezilla project's website. GET ON IT people!
An accurate explanation should be front page before the scare tactics have a chance to work.
Plus, users need an instant & easy way to identify if their version is legit to ease their minds.
Now concerning the bad guys... I'd suggest some sort of vigilante justice is in order.
Perhaps identifying the rogue servers and uploading something the local authorities might be interested in.