Question: I have my D7000 set to use its second SD Card slot to back up and I am shooting in raw (NEF). 

Every image is shown twice in playback mode, and when the images are imported to Photos (MacOS). This makes deleting individual images a pain. 

As it is copying the images to both cards it makes some sense, but the menu says "backup" not "duplicate" so I would at least expect the internal firmware to understand and not show the images twice. 

To clarify a little, when in playback/review mode, I see the images in chronological order, first for card 1 then again for card 2, so if I have taken images A, B and C I would see A1 -> B1 -> C1 -> A2 -> B2 -> B2 (1 and 2 represent the card slot).
So to delete image B I have to delete two images, once for each card.

Is this normal behaviour?

Firmware is
A 1.04
B 1.05
L 1.002

Answer: 
After the clarifications, what you describe is normal behavior. I simply leave the backup card alone and format it entirely when I am certain I won't need the backup copies. If you are concerned that the card(s) will fill w/ unwanted pictures and stop being able to record then I would just get a larger backup card (2-4x the size of the primary card).
That is perfectly normal behaviour based on the settings you described. If you want to reduce your time deleting duplicates on the computer, my suggestion would be to use a memory card reader and copy the images from a single card instead of copying the images through USB, using MTP(media transfer protocol).