No, you cannot disable your App Engine and still have Datastore working.
That being said, you only need App Engine enabled, you don't need to have a functioning app or even a deployed app.
Pregunta
Is there a "disable app engine only" button so I don't have a rogue hello world application hanging around on the web?
When I use this button it disables everything including datastore which I use separately as my haskell app database.
Solución
No, you cannot disable your App Engine and still have Datastore working.
That being said, you only need App Engine enabled, you don't need to have a functioning app or even a deployed app.