Right is right, wrong is wrong. Don't be ashamed for being honest and ethical. Never compromise your integrity just because the situation gets difficult. The Lord's tests aren't always easy, brother.
If anything, you can stand behind the fact that you did what you felt was right (even though it created an uncomfortable situation) in order to protect the company.
One of my favorite comments when I'm on the wrong side of a problem is, " I did what I thought was best in order to protect the integrity of the company; my number one priority. If I did something wrong, please help me to understand the flaws in my thought process; to show me that what I thought was wrong was in fact right. I just want to do the best I can do for you without crossing any moral or legal lines.
This happened to my Christian brother Luis. He was let go because he wouldn't "play the game". They would not give him an answer when he asked why he was let go. Now here's where his Christian heart shines. He sent out hundreds of resumes and went on countless interviews. When he was asked why he left his previous job, he was HONEST. He said he was let go and didn't know why he was let go. He didn't lie. Needless to say this cost him many, many jobs. Interviewers repeatedly told him not to say that and to make something up.
He was tested like never before, even resorting to painting houses for work until he found a job. He ended up at Chrysler earning 6 figures.
My point is, stick to your Christian guns. Don't go looking for a fight, but don't compromise your integrity either. Do what you need to do to be able to look at yourself in the mirror. Try to keep your job but if the business is riddled with unethical practices...do you really want to be there? If not, start looking.
/.02
Good luck my friend.