If you wear slacks and a belt, slip it into your buttoned shirt, Apple logo facing out and hidden behind the necktie. Hunch forward so not to make the shirt taut and show what's hiding underneath. Hold a cup or mug in hand to help block the view while giving backup support to the iPad in your shirt. Rethink your walking and positioning habits to accomodate the obscurity.
Haaa haa ha. Just bring your iphone if you have one for your 'bathroom breaks'. But really, do you really need to bring it in the bathroom with you? I understand if you're on a break and I've used my phone to look at the news apps from my phone. You coworkers are right though to give weird looks. Maybe once the novelty of the new item wears off people won't think its such a big deal.
If not, I actually was thinking about some sort of 'pouch pocket' similar to what you might get for a passport to tuck in your back since its a bit big. It shouldn't be too uncomfortable that way and would be pretty inconspicuous.
I wonder if there are off the shelf type pockets like that anywhere.