Probably not? It's pretty limited what you can do once jailbroken. Normally it's little apps and things that run on top of the normal firmware. Removing parts like the Amazon store would presumably require a more fundamental modification of the firmware that I'm not aware of having been done (but I'm a bit out of the loop).
I think iI saw somewhere a hack that would allow you to change the wallpaper you see when the screen is off, that's maybe a form of de-branding.
One thing that might be possible is to prevent the Kindle from communicating with Amazon servers. I'm not sure, but you could look into that.
Generally, most people on here are pretty fond of Amazon, and as such, are not interested in what you're suggested.
You can definitely jailbreak your device though. And pretty sure you can read epubs.
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