Mythology and deity work couldn't be any more different in modern witchcraft.
Mythology is, at its core, a story. A fanfiction, if you will, starring the gods that people worship. Trust me, I've read my fair share of Jesus fanfiction on the Internet, it exists and there is a market for it.
Deity work is a branch of witchcraft focused on incorporating the worship of and communication with deities. This isn't always necessary, as there are atheist and agnostic witches, and there are witches who do not incorporate their religions and beliefs into their practice. From open-culture polytheisms like the Greek and Norse pantheons (which is also known as paganism) to initiation-based monotheisms like Christianity, deity workers work with the deities they have connections to, and deities may come and go if they think the witch needs to learn what they teach or has already learned all they can teach the witch.
The difference is that mythology is not considered true (they're stories) and deity work is about working with deities in a witchcraft-related religious context. So telling pagans that their deities are as bad as they are in the stories is like telling a Christian that Jesus is bad because you've read Bible fanfiction on FFNet. And yes, it exists. I have seen terrible things.
Here's how I imagine mythology goes for the deities, because I wanted to share it with you:
"They wrote stories about us."
"They made it into a book."
"Well, that's nice."
"They...they think that's how we actually are."
When deity workers reach out to deities, the deities are often nothing like they're depicted in mythology. To go into a personal story, when I have interacted with Athena, she is...well, not really like the myths? She comes across as a gentle motherly/older sister figure because I feel her presence most when I am distressed. Zeus and Hera, from what I've heard by other witches, have a good relationship. Most of the relationships that are depicted as terrible in mythology are apparently not that bad, even healthy.
So why do non-pagans think like this? Because mortals just wanted to write fanfiction of their favorite deities and later generations thought that this fanfiction was how the deities actually were. It's like if aliens came down after an apocalypse, found those "Jesus is coming" boards, and assumed that he came and destroyed our civilization. Which is actually a really cool story idea, but overall not correct to how Christianity views him.
Sorry for using Christianity as a comparison, but its branches are the most common religions in my area so it's the religion I know the most about (other than paganism).