Interestingly, the Retina MBP has a combo Ethernet MAC/PHY + memory card reader chip of which they're only using the latter function. I would guess that either the decision to drop the Ethernet port was made pretty late in the process or the board designers were kept in the dark about the mechanical design until it was too late to pick a different part.

Also, a PCI-E lane actually is 4 pins :)

Edit: reply to dead - standalone memory card reader ICs are standard components. The USB SD ICs they used in earlier models would have been easier to route (than the PCI-E combo chip) and probably cheaper.