Refer to the mybeacon example in SDK 2.0 as a reference on how to bring up the part with a minimal configuration.
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> Would using GPIO_GLOBAL_INPUT_DISABLE help me in anyway?
This will high-z all GPIOs, so I don't think you want to do this.
> We also have a number of unconnected pins that I leave unconfigured for now, I would like to know the default configuration of those.
The default configuration of all GPIOs when coming out of power-on-reset is input enable. GPIOs that are not configured (either using BLE_PROFILE_GPIO_CFG or gpio_*) will be input/output disabled before application create is invoked.
> Is there any action I should take to configure the GPIO pins before allowing the sleep modus?
No, nothing needs to be configured. Input enabled with a pull-down is safe, though if something external to the chip is driving this input, then your system current will go up.