I’d say it’s rather a waste of time to try and discipline a bossy bunny or to dominate over it. A bunny is very different from a dog. Dogs want to please their humans, if only to get a treat or a favorite toy, but bunnies don’t care if they p.. their humans off.
I think she’s marking you as hers and that she’s guarding you. Like you were a bonded bunny couple. If the growl were unfriendly, I think you’d know it. My Yohio growls. Then he attacks with his claws. He used to do it with me but now it’s the broom that’s his enemy. There’s no way you could even suspect that growl to be anything but very un-friendly.The sounds bunnies make must always be interpreted in context.
Thumping or nipping when you stop petting a bun is not uncommon. The other day my bunny Yohio nipped the tip of my nose when I tried to stop petting him (I wanted to go back to sleep, he wanted me to get up and get him some breakfast. Guess who won? Yep, the bunny.)
It sounds like she’s still hormonal and from what I’ve read some girl buns can be territorial etc for more than 6 months up to a year after they’ve been spayed.