The only way I've found to do this is by using an email address for my device/desktop which I never use to buy books with. I can still update the device through the Desktop if I choose doing this.
It suits me because I only use Calibre cleaned epubs on my Glo, and not the kepubs, so I never have to sync. (I could use a plugin to convert my epubs to kepubs if I wanted, but I don't)
It's not a solution though if you do want to sync your device with your desktop and download kepubs directly; or if you want to buy books directly from your device to the bookstore.
I'd be keen on hearing if one can selectively download kepubs as well.
