As DoctorOhh pointed out, there has been a lot of discussion on this since the check was added. But, if you follow the instructions in the warning message, then you will have full support for yout Kobo Touch with calibre. Or, as DoctorOhh suggests, just treat it as a USBMS device and allow calibre to do the copies without looking at the database on the device.
An updated driver is being developed. Hopefully it won't be to much longer.