The interesting thing was that I contacted Nikon about the problem and I told them what I did to solve the problem, but I still asked them what was the metadata that caused the problem so I could perhaps write another script that was more specific to the problem, but they were not able to (or wouldn't) tell me.
I have written a script that uses exiftool to do all this, so let me know if anybody needs that and I will send it. What actually worked was to take another portrait-oriented photo with the D5000, of a white wall (or of a gray card), save the original metadata of the problem file to an XMP file, overwrite all metadata of the problem file with the gray card photo, then restore only the non-Nikon-specific metadata to the problem file. I also could not pinpoint what exact item of metadata had the problem, because it seemed to be one of Nikon's specific ones with binary information. Removing all metadata from a RAW file is an error, the file still can't be opened that way because some metadata is necessary to interpret how the photo was taken by the camera. Unfortunately I could not convert the files to DNG, that was one of the first things I tried, but after investigating the file itself for a while I found out that the problem lays on its metadata, as I first suspected, since only the auto-rotated portrait photos had a problem. Thank you very much for all the replies, I have now solved the issue.
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