As I understand it I should avoid going deep, and if I do I should angle my penis so it avoids directly impacting the cervix

Correct. Try doggystyle, this should angle you towards the anterior fornix, which should feel much better for her.

How can I encourage her to take more control during sex?

Understand that you are conditioning her in the classical sense.

Each time you have sex with her and it hurts, that is an unpleasant association being programmed into her brain, and each time reinforces that association. Eventually she won't want to have sex at all, because at that point her brain will think "sex = ouch".

This works in the opposite direction, too - if each time you have sexual contact with her, you express to her that there is no pressure for her to orgasm, you don't have to have insertive penis-in-vagina intercourse, and that you're really just there to make her feel good and have fun exploring each other's bodies, then she will instead associate sex with happiness, closeness, intimacy, arousal, and pleasure.

Take it slow with her next time, pay her lots of compliments, hold her close, and spend most of your time kissing her and doing "intimate touching" - fingers in her hair, caressing her cheek, that sort of thing. Go more romantic than sexual. And then end it with a tight hug and an "I love you." Followed by "want some water?"

What this will do is establish that sex and intimacy do not have an expectation of PIV or your own orgasm attached to them.

This will make sex a low-pressure, low-anxiety environment for her that she will feel more comfortable exploring and opening up to.

It'll take some time but remember: your job here is to be supportive and create an environment she can thrive in, not just take what you want from her and to hell with her feelings, comfort, or pleasure. She is a human being, not just a masturbatory aid.