As long as the Stories editor is part of the AMP Plugin, it needs to provide the controls for users to chose how the plugin would be used. The options could include these (or a variation):

• AMP + Stories: Serve AMP content, and enable Stories
• AMP Only: Use AMP only, hide Stories editor
• Stories Only: Only use the Stories feature, do not serve AMP pages

One possibility (discussed with @westonruter) could be to add a new "Operational Mode" complementing the Native, Transitional, Reader trifecta, with a "Stories" mode. The user could check only the Stories checkbox (Stories only), or check the Stories checkbox and one of the AMP template modes (Stories + AMP).