Well, no. Only nuclear BOMB summons the devil. The IAEA didn't mind all the normal nuke plants, just the mini-nuke. The daily operation of the plants don't trigger their devil meter. It's just that their response went way over the top.
It seems like the women with black hair and clothes are "witches" who were previously used by the professor. She probably develops "magical girls" in an attempt to study the metaphysical effects of things like irrationality and superstition in the world. Once these magical girls' effects on the world become too chaotic/damaging they turn into "witches" and are discarded by the professor. The professor herself is shielded from these effects by wearing an "anti-magic lab coat" as seen in chapter 8.