I think it could've been either the thing i don't get is why did they not just kill him?
Good question. I don't think there is a definitive answer.
My take is that the only person that Luciano and Costello would have trusted 100% to handle that job (Anastasia) was already dead. There had already been a number of murders and attempted murders so why bring more heat on the entire organization by trying to kill Genovese.
But I think the biggest reason is that they knew that they could hurt Genovese more by putting him in prison for the rest of his life.