Hi Andres,
In a sense, you have answered your own question: in your case the color change was a deal killer...so indeed, it has affected the value. Substantially might I add!
That being said, sit back and think about this for a moment. Color is, frankly, simply paint. Ignore the interior for a moment, and focus on painted metal.
How good is the paint, if original? Has it been well preserved? Have any parts of the car been repainted?
If a repaint job, how good is the respray? Was it a complete job, or a partial job?
What would you rather have, original paint in mediocre condition, some cracking, fading (some call it "patina") etc. or a great paint job that is not original or original color?
Very often, you'll see the exterior resprayed, but the engine bay remains original...as does the dashboard. This kind of thing would bother me, probably more so than a color that isn't my first choice. How do you feel about that?
My own opinion, and mine alone is this: do things right. There is nothing wrong with repainting a car, and nothing wrong inherently with changing the color to suit your needs, but it should be a good job. Do everything, or don't change the color. I don't care how perfect or Concours quality the outside of the paint is--if it is silver, I want to see EVERYTHING silver that is supposed to be silver.
Color preferences change over time, which is why 95% of new MB's are Silver, White or Black. Painting a car is a major undertaking and often owners will create what they want if they are investing the money. That's what I did--changed from 050 to 568. But it was done completely--you will not find ANY 050 on the car anywhere (save for the unrestored hard top in my basement that nobody but Peter van Es will see)
Personally, I'd look for consistency, accuracy and quality of the paint rather than be very concerned with if the color was changed. But that's from someone who did change their color...