The Sheldon Brown locking method puts the Ulock through the back wheel only, and inside the rear of the frame - the only way (aside from destroying the lock) is to cut out the rear wheel, and at the point of the wheel where the lock is - if someone wants to do that to get to your bike, well, they are crazy - can't pedal and destroyed the rear wheel where the motor is, meaning you just have to put out a notice to shops for someone wanting to replace a wheel with a motor in it!
On the battery, seems like taking it with you (along with seatpost) are the best options too, agreed there.
You can google the sheldon brown locking method, it is fairly widely accepted as one of the best options (through tire and frame of course would be ideal).