my tile data is already existing in a format I cannot change.
What kind of format is this? From my understanding all tiles are 2D images and as such can be edit at any time.
Could you elaborate or provide the file so we can see if it is possible to help you.
therefore: is there a possibility to change the map origin or do I
have to "rotate" the tiles during parsing of the map file?
Both is possible to a limited extend. Once you make the tile map you can set the origin to 3 points (Top left, Center, Bottom Left).
You will also be able to rotate the tiles by 90 degrees increments, after the tile map is made. I think this solves your problem.
The thing that bothers me is that the origin only says where a tile starts, it has no other job. So it shouldn't be rotating your tile, only move it around.
Could you provide an example?