Bobby wasn't always a good guy, even though the show makes it seem like they want the audience to always believe Bobby is "the good guy." He was willing to have Sue Ellen sign a fake paper stating she had no interesting Kristen's baby and no knowledge of the father. Then Bobby told her that she could never tell JR about this. Bobby was trying to illegally adopt a baby that he believed JR was the father of and his plan was to try to make sure JR never found out that Christopher was rightfully his. Both Bobby and Pam were willing to steal JR's son when they thought Christopher was JR's son. That's far worse than anything JR ever did to Bobby or Pam.