To disable Google Checkout for your account, just log into your E-junkie Seller Admin, click Edit Profile, delete your Google Checkout Merchant ID and Key, then click Submit to apply the changes.
The way our integration with Google Checkout works, they arrange for payment from the buyer independently of us, and then after checkout they send us a confirmation when they have completed the payment , so we just honor whatever they tell us about the payment status; when they report to us that the payment was good and completed, we presume that is accurate and process the order accordingly. If they're completing payments that should not have gone through at all, that would be an issue entirely at their end.
You may want to check your E-junkie Seller Admin > Payment Preferences screen, to confirm that you have "Wait for pending payments..." checked there; if that setting is un-checked, we would process orders as soon as we get notice that the buyer finished checkout, without waiting for actual completion of their payment.