Depending on your country:
If you want to make it stop, you can take evidence of discrimination to the authorities and the person/people being discriminated against can bring it up with the authorities for a lawsuit(s). This is a long and painful road, but if you have the backing of a portion of the staff past/present and you have hard evidence you can get the employer penalized(sometimes severely) and compensation for the discriminated employees. You have to prove it though, not just word against word.
If you don't want to fight or your in a country that doesn't have any laws against discrimination then leave and find anywhere better.
P.S. Please note that either course will likely mean you no longer work there, unless the penalty is to take the business away from the person and give it to someone else who supports the discriminated party rights.
Edit based on question edit:
If you don't agree with the underlying stance of your employer it's hard to stay working for them, without becoming disgruntled, unless that particular disagreeable belief is outside the day to day work activities. In this case I personally would have an issue benefiting over someone else's mistreatment, but that is the question you have to ask yourself if your not the discriminated race...if you are the discriminated race I wouldn't expect any different treatment for yourself.