You will go insane trying to develop on a 13 inch air. There is simply not enough screen real estate. However, the rMBP will be very good for this, and will get better I am guessing based on what I have seen.
As a CS student who uses a laptop with a lower-resolution screen than the 13" Macbook Air, I can assure you that you're wrong. For the first few years of school, your programs aren't much more advanced than System.out.println("Hello World");
The only time I have trouble with my 1366x768 screen is when I'm trying to develop for tablets, as having an emulator open pretty much takes up the whole screen - but you'll have that issue no matter what screen size you use, so just be aware that developing for an iPad will require you have a 2nd monitor unless you wanna have fun switching back and forth all of the time.
Of course, my roommate who has an internship was given a laptop with a 1080p screen. Seriously, that's an extra 180 vertical pixels.
Of course, one of my professors uses a macbook air connected to an apple display in his office as his main computer.
In all honesty, just make sure that the air you get has a 256GB SSD, minimum. If it's your main computer you'll run out of space faster than you would expect. Especially if you put a game or two on it.