To address your questions in order:
1) We do not issue thank-you emails, downloads or codes until the payment processor confirms that payment was good and completed; even without detecting anything "fishy", Google Checkout still sometimes fails to complete a payment instantaneously and may lag a bit (but still nowhere near as bad as PayPal has been lately!).
2) Inform affected customers that Google has not actually completed their payment yet and that the process is not always "instant", but once they do complete payment, then their link will be issued automatically. You can also use the "Send free thank-you email/download link/codes" function of your Seller Admin to placate irate customers.
3) If you wish to disable Google Checkout, just delete your Google Merchant ID and Key from your Seller Admin > Edit Profile screen.
BTW, in the case of PayPal payments only (not for Google, alas), you can bypass waiting for payment confirmation and just issue thank-you emails/download links/codes immediately by unchecking the "Wait for PayPal..." setting in your Seller Admin > Edit Account Preferences -- note that in this case, you would assume all risk of a payment falling thru after the buyer has already received their downloads/codes.