Dr. Bayliss has compromised personal fulfillment in medical research for financial security. Also, as he tells Kate in Act 3, he has known about Joe's guilt for awhile but has kept silent about it.
Chris Keller has compromised a sense of humanity for a rigid idealism. Forgiveness is difficult for him - he adamantly opposes his father's plan to forget the past and give Steve Deever a job when he gets out of prison, and denies his own father his absolution when he learns of his guilt. In his feelings of shame through his association with his father, he is willing even to give up his relationship with Ann without a fight.