They don't want to kill him. If they do, he would be replaced by someone more clever, like Visser One. It didn't take her long at all to figure out they were Human.
On the other hand, Visser One is the one pushing for a covert infestation. In a way she would be more dangerous, but on the other hand she can't morph. She also doesn't want to go out in the open with the war.
Better the enemy you know, than the one you don't. Therefore, they don't try too hard to kill Visser Three.