I'm scouting around for newer products and might have found a decent compromise:http://flashhavoc.com/yn-622n-tx-first-image-emerges/
It looks like Yongnuo is going to release a newer version of their old YN-622C sometime later this month or early next year. The unit is called the YN-622C-TX and acts only as a transmitter which interacts with the existing YN-622C transceivers. The link above does show "Remote Shutter Release" as one of its new features, which the old YN-622C doesn't have.
So it seems to me the setup would be:
YN-622C on camera hotshoe
Speedlight on YN-622C
YN-622C-TX acting as the transmitter remote
(Nothing connected to camera's 3-pin)
It seems this would resolve the following:
1) ETTL - Check
2) Camera hotshoe isn't taken up in such a way that you can't mount a flash - Check
3) No extra receiver needed for remote shutter - Check
4) No cord needed to connect receiver to camera pins - Check
5) Remote shutter release functionality - Check
This system still wouldn't leverage the RT radio functionality that's already built into one's 600EX-RT, but it seems like the cleanest one I've seen so far.