In terms of positive PR, they could have gone with:
1) Put up a warning that the device is counterfeit and will only work for another N times (after which, simply refuse to work with it - don't modify it outright, though given the technique a temporary modification may be required).
2) Ask users to take a picture and name the vendor and product in a tweet using hashtag #fakechip (or whatever marketing comes up with)
3) Every first tweet of the vendor/product combination is rewarded with a free genuine FTDI replacement chip.
4) Sit back, collect the list of naughty companies (pass on to legal if bored), watch the build of goodwill, the discussion of fake vs genuine swell.
Instead, the discussion is now much less about counterfeit vs genuine chips, but about FTDI doing something that apparently is hugely polarizing (some people supporting the practice, most others wondering wtf FTDI was thinking) to electronics enthusiasts/integrators, security experts, and even legal eagles who aren't sure whether FTDI did something clearly illegal any more than whether they did something that was clearly legal, and a secondary discussion on what to replace FTDI parts with. All rather more negative bits of PR for FTDI, even if further out into the future I think this will have been seen as a good move.