How to remove quinoa bitterness (with many restrictions) doing chapatis
You are unable to do anything about it. The bitterness in commercially prepared flour is from the fact that they don't thoroughly rinse the saponin from the outside of the seeds. Once it's milled in, there really isn't anything you can do about it, doubly so when making a bread that is basically flour and water. 

So you have two ways to fix it. One is grind your own quinoa flour, which is not too hard, after you make sure that it is rinsed all the way off. The second is to use a different type of flour, like tapioca.