My experience is that many small, non-chain hotels in Europe prefer cash or cashier's checks, but will hold a room with a credit card. No red flag here for me.
However, I agree with the OP in not wanting to email a CC number. I usually email the hotel, get their fax # and send it that way.
Some of our nicest hotel stays in Europe have been the small, private places that still survive with a cash preferred policy.