It all depends on the models of the cards and more specifically their read speeds. If the CF has higher read speeds, the only benefit you get is that you'll be offloading files from it faster (but this also depends on the card reader's speed and connection). USB 3.0 has the bandwidth to accommodate even the fastest cards available today; 2.0 can potentially be a bottleneck. As already mentioned, if you've set the camera to write the same format to both cards, it won't matter which card you copy your images from - the files will be identical.

Edit/update: Any transfer between devices will be limited by the slowest link in the chain, so in your case, getting a faster SD card reader for example won't help with this particular SD card since that's how fast the card goes. USB 2.0 will be a limiting factor indeed for a CF reader - it's specified at 480 Mbit/s which is practically 60 MB/s or less. A good bet would be to get an external Thunderbolt card reader given you don't use the port for something else and given you can find one for a reasonable price (since they're not as commonplace as USB readers, making them more expensive). It's up to you to decide if you want the speed of an external reader over the convenience of the built-in one. You can still buy a USB 3.0 reader (it will fall back to 2.0 specification on this computer) and although it won't give you any benefit over 2.0 right now, you can carry it over to a newer computer in the future.