As an update. I didn't take the car in for service right away not because I didn't think I needed to but because I just didn't have time. After driving it for about 1 week and about 1 tank of gas the idle had resolved and is perhaps better than before.
If I were to guess, the ECU got reset at the dealer when the rear diff. was replaced and the ECU seemed to run pretty poorly before it "relearned." I'm still not enthused about my reliability but at least my rear diff no longer whines/makes a burning smell, and my car doesn't rock like drunken water buffalo at idle.
Anybody else out there with a really rough idle following an ECU reset?