There is nothing currently implemented to disable the WebStore confirmation email. Since WebStore is best at selling download products the internal confirmation email has generally been very important because the PayPal email does not have a link to the order detail where the customer could download the product so it is generally not sufficient when selling download products.
I suppose if the order has only non-download items then the WebStore confirmation is less useful. But, the other consideration is that not all payment providers send their own email like PayPal does. For example when using Authorize.net the WebStore email is the only confirmation email sent to the customer so any disabling of the WebStore notification would have to be smart enough to know that the order contains no download products and the payment method was PayPal, if either of those is not true it should still send the notification.
I "could" implement a site specific web.config/user.config setting to support disabling it in that scenario. I estimate that it would take me less than 2 hours to implement and test. At minimum I will log this request in our project tracker for future consideration. For a small donation/sponsorship of the development effort I would consider making it a priority and promise it for the next release or even could provide you with an updated deployment package after it was implemented so you could get the functionality even before the next official release.