According to Amazon selling policy, you cannot use emails or any other marketing messages encouraging users to leave the Amazon website.
If you enabled Magento Sales Emails for orders, you will need to turn them off. To do it, please navigate to System > Configurations > Sales > Sales Emails > Orders in Magento v1.x and Stores > Settings > Configuration > Sales > Sales Emails > Orders in Magento v2.x.
If you want to disable confirmation emails only for Amazon orders, please switch off the "Magento Sales Emails" option per specific Store View in your Magento. Then, select this Store View as a data source for the Channel Orders in M2E Pro under Amazon > Configurations > Accounts > Order tab.