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I tend to use the command line when mounting or unmounting devices (habit from the past), so my experience is based on that. If you use umount to unmount the device, then it'll act the way the OP says. However, as mentioned above, using the eject command does allow you to use the device as it's charging (eject /dev/sd*, etc). If you're using the GUI, then avantman42's suggestion of using eject is the way to go. You should get a device icon turn up on your desktop when you plug in the Kindle, and if you right-click that, you should find various items, eject being one of them.
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