It's still a lot of juggernauts for one node. I'd be interested in lining up thirty to fifty juggernauts, just to see how long it would take them all to depart. I doubt more than a handful would be able to complete the intrasystem jump, approach the Gamma Draconis node, and jump again, by the time the shockwave hit. Five, maybe ten at the outside, if the Gamma Draconis node is way the hell out there, but not more than that. Unless they made an intersystem jump from right there, most of that fleet got toasted.
That said, logic and reason might not have been the guiding principles behind the decision. As alien as they are, the shivans might have come down with a bad case of human desperation at the last moment, looking for any chance, no matter how slim, to survive their own superweapon. Just a thought.