It's very unlikely that he used a compact chainset. I'd think he would want to maintain the capacity for as much top-end speed as possible, especially on a stage when Nibali might try to get away from him on the downhills. And even those who use compact cassettes (me included) tend to dislike the 16-tooth drop between the 50 and 34. So I'm betting on him being on a 53-39.
However, the point about low gearing is well taken. If you watch Wiggo's cadence up the long climbs, it's an object lesson in using his aerobic fitness to save his legs and maximise his endurance. Struggling up hills in too big a gear is a mug's game.
And just to add a controversial note I'd recommend a triple to the heavier rider. Gives the opportunity for a big range together with nice close ratios, which a compact with a big cassette does not.