This has nothing to do with the arduino IDE, and not much to do with Arduino. It turns out that FTDI had an updated driver distributed which would break "clone" FTDI chips. (The FTDI chips provide USB/Serial communications in arduino boards older than Arduino Uno.) (this driver has since been withdrawn, due to really strong feedback.)
You can read a summary here: FTDI Screws Up, Backs Down | Hackaday
And more than you ever wanted to know over here: FTDI driver kills fake FTDI FT232?? - Page 1
As it turns out, not very many clone Arduinos still use FTDI chips (real or clones); they're not used in the real Arduino Unos, and were not particularly popular as an alternative USB/Serial Driver (where cp2102, prolific, and CH340 have been cheaper, more common, and more commonly cloned.) The main danger was in buying "FTDI serial adapters" that contained clone chips. (actually, it could be that there were some "more official" Arduino clones, and Nano clones, that still use FTDI chips, and could have been using cloned chips. And of course, duemilanove clones...) (You'll notice that the article you reference is about Nanos.)
It's unfortunate that Arduino is being blamed for this anywhere; they had nothing to do with it.
For those of you who may be interested, the forum on Timescapes.org is an excellent resource for anyone interested in timelapse photography and/or building motion-control systems for cameras used in timelapse or stop-motion animation. There is a wealth of information concerning both software and hardware implementation, often using Arduino based controllers, and a very mature, patient and helpful community of contributors.