I'm with snockit on this one. With the benefit of hindsight, I think the use of the JtR character is perfect, because it beautifully foreshadows what the shadow war is really all about.
Sebastian/Jack killed because, from his point of view, he was doing a good thing ... the right thing.
The Vorlons sought to bring the younger races into order and obedience because, from their point of view, they were doing a good thing ... the right thing.
The Shadows sought to create tension and war between the younger races because, from their point of view, they were doing a good thing ... the right thing.
Jack was a good character for this because history just views him as a monster, which of course was how we viewed the shadows at this point in the story, whereas JMS showed him as far more complex than that and acting on his point of view rather than a monster who simply killed for the sake of killing.
And as far as Sheridan and Delenn were concerned, I think they didn't question the Vorlons' tactics because they still viewed them as the key to everything ... don't forget Sheridan had only just been let in on the shadows presence and what they were up to. As far as they were concerned, without the Vorlons they didn't stand a chance.
All just MHO of course.