Go for the first option.
If the app you uploaded to Google Play uses Google Play for in-app billing, then you have no issues whatsoever, even if there is coding and permissions etc. for Amazon payment inside the app. Google doesn't analysis this. And event if they would, you are on the save side, as you only use Google Play's in-app billing.
You can even improve this option by using Android Studio and Gradle build. It allows to package only those artefacts, that you need for certain build variant. In your case, you can have a single version of project and configure Gradle in a way, that it creates two apk-files: one for Google Play and one for Amazon with respective payment logic in them.