Roth planned to get rid of Michael after getting his two million dollars, so he did it for a back up plan. He figured if for some reason his plan to kill Mike in Havana fails again, he get him in the US with those senate hearings. He decided to have Frank killed in a way to make sure Willie would get the message so he would cooperate with the FBI to testify against Mike. Frank accidentally survives and goes with the witness protection plan of the FBI himself to get Michel because he thinks Mike has double crossed him. Mike really didn't want to kill Frank when he told Roth about killing him, he mostly wanted to see Roth's reaction toward the matter.