Actually I'm planning to leave my battery on my bike when I park it for few hours.
But the battery would be hidden inside the brompton bag.
I've tried to hide as much as possible all the "electric" components visible from my bike. People looking at my brompton just think that my motor is a dynamo hub
Hope however that the thieve wouldn't want to steal this bike...
Edit:
On my full size bike, I've always parked my bike with the battery visible:
No one never ever tried to steal the battery box. I've got my seat stolen, my toolbar, my bike pushed... but nothing on the battery box. I believe thieve wouldn't know how to sell it so they don't even try.