This is debatable.[1] After hearing about this through NPR I initially thought that it was terrible; however, after doing more reading it seems to be unclear what kind of effect this is actually having on their economy.[2]
Most would argue that "effect on their economy" is a means to an end, and that "effect on the well-being of people" is the end itself. In that case, economic analysis can fall short. Friends of mine have personally spoken to rural Andean farmers who can verify that the price rises in quinoa can cause more problems than they solve.
How does that work? Food security should increase rather than decrease. Subsistence farming is a living that can be extremely hard to the point of starvation when anything goes wrong.
Sometimes a "more problems" verdict neglects the idea of different qualities of problems. More money usually comes with a higher quantity of problems, for example...
[1] http://marcfbellemare.com/wordpress/2013/01/quinoa-nonsense-...
[2] http://ain-bolivia.org/2011/05/bolivian-quinoa-questions-pro...