Bones tv show need help understanding an episode!?

He was not pissed because he Loves Bones and she loves her father. her father is involved in shady business, but his heart is in the right place and the guy he killed probably had it coming, it may have been someone involved in the murder of his wife. But Booth knows that he should pick his battles and that Bones dad is not his biggest problem, so if him getting away will lift Bones' spirits then it makes him happy.