When her occult bookshop is burned down, an angry, self-loathing Witch must stop a secret organisation from murdering powerful witches.

“Also I?m totally not sure how she?s going to take down this organisation, other than she?s more powerful than she knows.”

This statement brings to mind a deus ex machina device where she suddenly learns she’s more powerful than she thought before and then she wins. Rather than have her win because she’s more powerful, I suggest making her use her wits to use the power she already has in order to defeat her opponent. Unless a major plot point is her trying to increase her power to be strong enough, then that’s my suggestion.
For example, where does the organization get its resources? She can attack them by attacking their resources. Why do they hunt witches? Is it based on misinformation or fear? Can she use compassion and information in an attempt to change people’s minds?
My point is that it doesn’t have to end in a big, CG filled battle(maybe with a sky beam?).
Just some things to think about.
Is this a sequel? Do you plan to make it into a franchise?

I agree with Nir Shelter in that the concept has a good hook. But for the logline maybe you could be a little more specific? How exactly does she plan to stop this organization? If they’ve been murdering powerful witches, how can she stop them?
Also, something to think about is the antagonist. First, consider choosing and developing a character, the main face of the opposing organization. Why do they want to kill witches?
Something I do for all of my stories(which are also Fantasy/SciFi) is create a logline from the perspective of the antagonist. What motivates them?