Even that one time they weren't trying to kill him. Beeman merely intended to use the Lute song to incapacitate Zak and Argost. He was going to turn it off before it became lethal. He just set his estimate for how much they could take higher than Dr. Grey did. For all we know he was right, but he was the only one of the two of them willing to risk it.
They never wanted to kill him, but the fact that he could destroy civilization would mean that his life would be weighed against the numerous resulting casualties in a do or die situation.