It's all politics-

Black Pete took part in the murders of several Columbo guys but Chin gave him a pass despite the bodies turning up at that building he owned

All he did was plead ignorance and Chin loved him (most likely due to the amount of money he bought in) and Pappa instead was collateral damage/ who took the fall

As for Jimmy Burke, whilst he was never made, he was almost like a captain himself. The same way Angelo Quack Quack got a pass when he done the attempted hit on Casso. Casso instead went after all the lower level guys involved (granted Angie was dying anyway)

Usually if a guy is too valuable to be killed, a big fine can sort out any grievances