I didn't see a reference to whether the OP was comparing retina machines or non-retina machines, but the CPU in the 2012 model should be the same in both models as they were updated together.
The benchmark shows that the expected CPU performance will be more or less identical. I agree benchmarks are more or less pointless (subjective comparison at best for real world use), as the rest of the system has a huge effect on perceived performance (SSD vs. HDD, GPU model, etc.). Without more context I would call it a draw, and if the OP needs to run the CPU full bore for long periods, I doubt there will be much of a discernible difference.
Frankly, depending on the software used, a dual core machine with a higher clock speed could outperform a quad core machine with a slower clock speed, if the software is not designed for multi cores and multithreading. Much of the software that I use in my analyses is written this way. Making the analysis support multiple cores and threads seems like a good idea for future plans, but it makes things more complex to hand it off to the next student that may or may not have programming experience.
To me the difference between the machines are amenities, wireless ac vs n, TB2 vs TB, etc. It's not as though many ISPs are allowing users to download at rates that are going to saturate wireless n, and likely won't be for some time. Personally TB peripherals just don't fit my budget.