ATA Drive vs Flash Storage
It depends on what kind of programming you're going to do. Especially if you going to test the programs that you're developing.

Any of these "is it worth it" questions are going to be highly subjective.

I would think that an average programmer would value the SSD more than the extra CPU speed, as compiling/building involves a lot of small files which the SSD will handle faster than the ordinary hard drive. However, a RAM drive would be faster than either disk. So it depends on your setup.

Also remember that the MacBook Pro is a 2012 model compared to the 2015 MacBook Air, so you cannot compare the CPU as simply 2.5 Ghz vs. 1.6 Ghz. This could lead you to believe that the MacBook Pro has a CPU that is 56% faster than the MacBook Air - however benchmarks show that the CPU is really only about 4% faster. The GPU is also faster on the Air (Intel HD6000 vs. Intel HD4000).