Yeah, I also dislike KOReader's folder based approach to listing books on device.
Anyways, don't remove jailbreak from your Kindle. Just use what you like (stock reader software). You never know what the future brings and when the jailbreak and freedom to customize and add stuff will bring you some benefits.
It is always better to have something and not use is it or barely even use it then not to have if at all.
This PW5 is the 4th Kindle I've owned and all of them had jailbreak, even before KOReader existed