I think that I agree with the majority opinion, that Queen Chrysalis is more evil than Discord. However, as all of the arguments supporting Chrysalis have already been stated, I want to bring up a few points defending the claim that Discord is the worst of the two villains (before he was reformed).
First of all, Queen Chrysalis only impersonated and controlled ponies so that her fellow changelings could live. Anypony would be willing to do anything for their family when in Chrysalis' situation. Discord, on the other hand, had no motives behind his actions except for his desire to be entertained, and was willing to do whatever he wanted with the ponies of Equestria, without any care as to what they were feeling.
Also, note that when Queen Chrysalis attempted to gain control of Equestria, she simply impersonated Cadance and then caused Twilight's friends to distrust her. However, when Discord escaped and took control of Equestria, he purposefully not only controlled the Mane 6, but made them be the exact opposite of who they were, ultimately making none of them ever want to see each other again.
Also, remember that even after Discord is reformed by Fluttershy, he continues to toy with other ponies' emotions without giving much thought.