On my transam I carried my netbook in a neoprene case inside a bubble wrap envelope inside a front Ortlieb roller. I had no problems. I'm not sure the bubble wrap was needed but it worked anyway and I had the space.

That should work for you with a rear pannier. Or to beef up the protection what about packing it the same way then stuffing your sleeping bag round it for more protection from impacts if the bike got dropped.