With the survival of the Terran and Vasudan species at stake, the GTVA didn't want to take chances on a phenomenon that had never been properly observed before. The Lucifer's explosion was probably bigger than a normal Orion's. Maybe the Capella-Epsilon Pegasi node was more stable, and would take a bigger explosion, than the Sol-Delta Serpentis node. A gutted Orion stood a better chance than freighters, of getting the bombs safely to the node.
Why did they jump in so far away? We can only speculate, but maybe intrasystem jumps don't work for large-mass capital ships, when they are too close to a node. Karajorma's explanation works, too.
EDIT: Yes, I meant Delta Serpentis...