I'm not sure I'd agree with that. Having worked for a major component distributor, I know that they wouldn't buy grey market stuff of parts of one of thier official suppliers. With that in mind, as long as you buy from an official supplier you won't have a problem with supply and you know your product will always work just fine.
I think FTDI are problably in a difficult situation in that if their driver didn't actually alter the counterfeit product, but did stop it from working, it seems that people would still end up with the same situation. ie Their product no longer worked. Then again, why should FTDI allow the market to be flooded with counterfeit parts?
You could argue that they could roll back to older drivers if they didn't change the EEPROM, but then again, you can use the FTDI tool to change the part's EEPROM value back. I honestly don't know what's harder as I stopped using Windows years ago and can't remember how hard it is to find and install drivers. From FTDI's persepctive, at least this has brought a big issue to light.
As far as the legal standpoint is concerned, you'd have thought that they would have consulted lawyers about whether or not it was legal. There's lots of opinions stating catagorically one way or another that what they have done is legal or not, but I'm assuming no-one really knows. It would seem that Apple has done essentially the same thing previously and it didn't cause them an issue, so why would it affect FTDI? (Honest question, I am no lawyer so there could be a good reason why this is different.)
As for changing to other suppliers, who's to say exactly the same thing won't happen there? I'd bet that in a few weeks this'll be forgotten about. People like Arduino will have to replace a load of boards with counterfeit parts and hopefully learn a lesson in legitimate sourcing. Maybe FTDI will look back on it and learn a lesson if the publicity does affect them, but I'd be fairly surprised if any major manufacturers changed from FTDI because of this.