I'm due to revisit Crusade soon, now that I have some of the books about it, but from what I recall, after it was cancelled, JMS said the whole first season was basically a bait and switch. We're led to think it's about the search for the cure to the Drakh plague but that would be resolved and then we'd find out what the show was really about. If I remember that correctly, it was a pretty risky thing to do. B5 wasn't such a popular property that JMS could safely assume that an audience would get hooked enough by Crusade's original premise to stick around for something bigger that they didn't know was coming. That could have been an issue regardless of network interference.