After trying to install the system again to see if I could replicate it the issue, I made a usb key where the firmware-iwlwifi package contained only the 1000-5.ucode file. Initially the interface asks about 1000-5.ucode, however when I try to load the non-free firmware it seems like the driver gets loaded, but the curses interface does not acknowledge this and loops back to asking about the non-free firmware but now it's not asking about the 1000-5.ucode file just 1000-4 and downwards. If you then choose "No" on loading the firmware you can continue to configurate the wifi-adapter. So it seems like there's some bug with the interface not going forward even after the firmware is loaded.
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