What FTDI is doing is insane.
Yes, FTDI does have a problem with the crap clones, but inserting things into people's data streams is NOT, in any sense, a proper response. It's slightly less insane than BRICKING people's hardware (their previous solution), so I suppose it's a step up, but it's still completely nuts.
Refusing to work with non-FTDI hardware would be perfectly reasonable. Log messages if you have access to system logging facilities (I'm pretty sure drivers can log to SYSTEM log in Windows).
But mess with people's data? That's insanity. You NEVER mess with people's data. ESPECIALLY when the data belongs to someone who probably has absolutely no idea what the hell is going on.
They are once again breaking things that don't belong to them. With any luck this will backfire on them just as badly as last time. I'm hopeful that this time Microsoft will get in on the act and beat them soundly around the ears so that they stop this shit.