You could do this in the config file, but it's easier to make this change in game (although you may have to do it each time you switch to it). This requires that you have a docking port pointed in the prograde direction. If you do, right click on that, and select
Control from here, and you're done. The gimble will flip, and everything will be pointed in the correct direction.
If you don't have part that you can do a
Control from here on (and is pointed the correct way), then it is possible to make the change in your persistence file. In a text editor, open
%KSP_DIR%/saves/<save name>/persistent.sfs, and under the
VESSELS section, find the probe you want to edit. Find the
PART section for the probe body, and change the value for
rotation. I don't know the format for that value*, so this could use some experimentation, but set it to
0,0,0,-1 and see what that does.
*I don't have time right now to test this to tell you for sure what it should be, otherwise I would.