As far as I know there is no way to disable that checkbox through the cloud console.

Perhaps we should take a step back and ask why you need to disable it? If you are having trouble with a specific application issue, the answer might really be to manage the settings of the scanning modules affected. Those are settings you can at least control from the cloud console.

If you want no cloud reputation services at all, perhaps you need a product that has on-premises management, not cloud managed. :-\