You can Unlink your app in the Environments settings on the developer portal. That way you app will be disconnected from it’s deployment and no longer available. This has no impact on your project itselfs.
If later on you want to be able to redeploy it to the free cloud, you can connect it again to the free cloud.
If the published app is in Sandbox, it will get automatically stopped after sometime and resumes only when you hit the app url.