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.
In "Guess Who's Going to Be Dinner?", Zak and Fiskerton break into the "Experimental Weapons" vault. When the Big Bad of the episode is chasing them, the handful of weapons Zak grabbed prove to be useless...except for when they spill out of his hands, and it was revealed that his mom's fire sword was among them! First, why was one of the family's MAIN WEAPONS/one of the most valued possessions Drew had in with the useless junk in the Experimental Weapons vault? Couldn't it have been put somewhere more secure? And that sword is at least three feet long; how did Zak not notice he had it with him along with the other weapons? The way he says "Mom's fire sword" sounds like he was surprised (albeit relieved) to see it.