If you have NickelMenu installed, you can set up an entry that reboots your Kobo. I find this keeps the database corruption from happening since the databases will be properly closed before the USB connect. I used 3 entries so I could reboot from the home screen, books or reading.
Code:
menu_item : main : Reboot : power : reboot
menu_item : library : Reboot : power : reboot
menu_item : reader : Reboot : power : reboot