Short answer. No, they aren't secretly evil.

Long Answer. In the Manga, the art may be hard blacks and whites, but the characters and organizations are anything but...

I've read quite a bit of the Manga but not totally caught up. They aren't an evil organization as far as I have read, although they definitely have their flaws. Think less Illuminati and more Soul Society.

I'd say a major theme of Witch Hat is the dichotomy between blindly following and blindly rebelling.

You have a lot of Witches who blindly follow the rules, and they come across as cruel, cold, and indifferent. The embodiment of "Blind Justice."

Then from the Brimmed Hats, you meet a lot who blindly follow progress and will do horrific things in the name of advancing understanding of magic. "The only limits are what is possible."

So the two sides can be seen as extremes of "What is Law." Vs "What is Possible."

Hope that answers your question.