Why didn't you test the original blue/green? What were your findings on that? You should have applied the colors as present in the patch, as these were the colors agreen upon in the original commit, which were blue for deleted content, and green for added content. Those had been tested by various users, both color-blind and not.
Green has a meaning of "Go" or of "this is ok" in many cultures. Making either side green gives a bias to the diff. Similarly with red. Red means "Stop" or "this is not ok". Many people associate red with blood, and green with nature.
- Ryan