As mentioned in the original post, digital optical out is no longer, so you'll have to enlist external help (as is the norm with new Apple hardware) in order to retrofit. As Al Griffin mentions, one method would be to connect the ATV to the TV via HDMI, and then optical from the TV back to the AVR. (Assuming the TV can actually pass through 5.1 channel audio, the 5.1 limitation wouldn't matter since the AVR in this particular example only has optical inputs anyway.)
…but that’s assuming the trigger has actually already been pulled on the ATV4.
Outside of a new remote and an A8 processor that was introduced last year, I think it's a bit of a stretch to call the ATV4 an "upgrade." (See for yourself here: http://www.apple.com/tv/compare/.) Those who waited for ATV4 *STILL* didn’t get 4K, hi-res audio support, DLNA support, a gigabit port, nor live TV. (Side comment: Four gens in and I still don't get why it's called "Apple TV" if it doesn't actually offer you live TV broadcasts. But anyway...)
So when considering this particular configuration (recall the FiOS STB, Oppo, and earlier ATV), I see more value in replacing the AVR with a new(er) one that's HDMI-capable (especially for the Oppo!), instead of "upgrading" to ATV4.
Besides, once the autonomous, initial surge of must-purchase-new-Apple-product wanes, the price of the ATV4 will only drop.
Happy media enjoyment!