To me, the biggest aftereffect of 3039 is one that's often overlooked: It marked the public unveiling of the Com Guards, and their eventual stationing of forces all across the Inner Sphere. Not only was this a huge win for Comstar, but once it became the new 'normal' in the populace's eyes, after the Schism it gave the Word of Blake a vast multitude of small bases in areas they had influence. I'm sure we can all agree that the Jihad would have had to follow a very different path if the Blakists hadn't had access to all of these staging areas.
You ask me, the real winner of the War of 3039 was Myndo Waterly and her followers. Aside from the aquisition of Anastasius Focht eventually proving her downfall, she really knocked it out of the park with this one.