The solution is further down the same page:

https://github.com/jedisct1/dnscrypt-proxy/issues/98#issuecomment-62636551

I had a problem flashing the zip (made by qwerty12) in the link so you may need to extract the contents to the relevant directories (in /system) and make sure they have the correct permissions. I used Fx explorer for this. You obviously need root to do all of this.
Then set the DNS to 127.0.0.1 (I used Static DNS for WiFi but many programs will do this)
That's all it should take.
I have posted in the same github link confirming it works fine.