This was something I was wondering.
Even though I don't doubt this happened, the whole summary and concept sounds too much like a cheap scare tactic. The mechanisms for cyanide production had to come from somewhere. The cyanide production had to either be natural to the plant strain originally or involved with whatever was added. What you say is similarly true for yeast. Fermentation of alcohol has to occur in anaerobic environments as otherwise yeast produce other compounds. Still more research needs to be done.
If what was added, kill use of this strain while examining it as one would a medical treatment/substance that passed FDA inspection, but started killing people.
If else natural, could be a coincidence that this was GM. Perform studied/experiments against un-GM versions of same plant strain to see if this is the capabilities of the "normal plant" in similar environmental factors, or a mutation in part of the plant's genome that should not have been influenced by the GM modifications.
Else a combination of the two, study to see how to prevent this from happening again. If unprovable either way, release a version that removes the capability to produce cyanide unless it is a necessary requirement for the plant to survive.