I'm not a chemist but I'm pretty sure it has to do with the things that happen to starches in general. In particular, the chemistry isn't about the wheat gluten, it's about starch. Thus, if you feel your quinoa pasta is coming out too gummy or mushy on the outside, you might try it. (If your pasta is already mushy or gummy, how much worse could it get?)
I use vinegar in pasta water with Barilla Plus, which has a lot of wheat but also other stuff, and it causes no problems. I will also say that with really good pasta like that it's a little hard to tell the difference. I have a box of fancy Italian super-starchy pasta that I should try it on.
edit — whoa I just re-read the last line of your question, and now I'm confused. "Keep it starchy"? No, that's not what acid does. The intent is to keep the pasta "pasta-like" in the water; to make sure that the outer layers of the pasta don't get "waterlogged" before they firm up from the heat. Is that what you mean by "keep it starchy"?