IOS 10.0.1 on an IPhone 7 with WhatsApp 2.16.10
WhatsApp is using the new CallKit VOIP framework that allows apps such as WhatsApp and Skype to integrate more directly with iOS. This allows, for example, incoming calls to show up on the lock screen like cell phone calls do. As you've discovered it can also integrate with the native Phone app's call history ("recents"), contacts and so forth.

There is no setting to disable this as it is a fundamental change to how iOS handles VOIP apps.