Hamlet doesn't kill Claudius at this point because he believes that Claudius is praying. He says that killing the king NOW would be "hire and salary, not revenge!" He simply cannot send Claudius to heaven, where he would surely go where he killed just after praying and purging his sins. He thinks that would not avenge his father's murder, because Claudius killed Old Hamlet without giving him the opportunity to pray, and therefore, Hamlet decided not to kill Claudius.
