Whoa! It just occurred to me: If Marco had destroyed Visser One and saved his mother, his mother would then have had control over a "Nova-class Empire ship" (which appears later in the story under her orders)! Wouldn't the other Yeerks continue to obey her orders? They can't tell that the Yeerk in her head is gone. She could have ordered it to blow Visser Three's blade ship out of the sky! She must know all about the Yeerks' plans, security, everything.
I really think that Marco could have ended the war right there. And given all the times Jake and co. went for super-long-shots, they certainly should have gone for this one.