How do cinematographers do super zoom out shots?

Some cinematic shots like this do use CGI or transitions between consecutive shots taken from further and further away; but this one looks purely physical.

2012 is a bit of a transition period for arial camera work. A only a few years before, they would have had to use a helicopter, these days they'd just use a drone. As the shot is not just a simple 'zoom' it has a flying arc, I'd put money on it being a drone. To use a helicopter they would have had to start on a crane, then CGI'd across to a helicopter, otherwise there would be far too much down-draught for the close-up.

You can see down-draught in the water as it pulls away - you can even see spray and a small wave lifted, pushed opposite to the water flow direction, as well as a general water disturbance as the shot moves out.
I've never seen a drone working over water, so I don't know how much down draught they can generate, but the ravine looks a bit of a squeeze for a helicopter.
If you study the first part of the shot carefully, it's logical that this is where the camera starts, directly over that disturbance you see as it moves away. I think it's a zoom lens. You see three kind of step-wise changes in the lens tilt mechanism as it starts to move horizontally. [These days you can program in that kind of move, which the software can then interpolate to keep everything nice and smooth.]
I think they cover the zoom-out through this transition, where it's harder to spot. It also would add to the feeling of acceleration as the larger move begins.
Further supporting theories for it being a zoom lens are - the start of the shot is really quite stable and starts quite tight, it's an elevation change only, similar to a crane shot; and they wouldn't let a drone so close to an actor [or anyone]; the little 'push wave' you see as it moves away looks a long way away from camera, which adds credence to the lens being at its widest by then.

Note that the type of drone used to swing a 35mm cine camera around is nothing like the tiny quad-copters you can get these days. They stand 3 or 4 feet tall, and almost as much in circumference. They have 6 or 8 rotors of maybe 8-10" each - not encapsulated either. There are strict protocols in place to ensure no-one is underneath when it's low and established emergency procedures for if one does start to fall.

Skyfall is generally thought to be the first movie that really used drones [the opening motorcycle chase across the rooftops] but as Bourne Legacy is the same year, it wouldn't surprise me if it was done the same way, just to lesser applause - it doesn't form a major feature of the entire scene like Skyfall, it's just a single shot.