We can try to engineer these plants to die after some time and not reproduce but it wont hold forever. That's why I think these plants should only be grown underground or in very remote and starving areas.
I think the key is to encourage genetic diversity with genetically modified organisms as well as normal strains. Also to avoid monoculture agriculture. This helps avoids the problems of resistance (like with pesticides).
You can breed potatoes to be resistant to disease and those potatoes can become toxic to human beings. In other words traditional breeding can be dangerous just like genetic engineering if you encourage a plant to produce something toxic to human beings.