(Speaking of which, kind of a pity we never got closure on Crusade. An abrupt "The Drakh Plague was cured, and Humanity and its allies lived happily ever after" is kind of unsatisfying.)
Actually, from what we now know, the Drakh plague would have been cured very early in the second season of
Crusade, with the true arc of the series -- Gideon and the
Excalibur crew going renegade from EarthForce while fighting against a secret faction attempting a governmental takeover via Shadowtech -- coming into play at that point.
The plague itself was simply a red herring, a plot-device to kick off the series in order to get to what the show was truly, actually about.
J. Michael Straczinski has said that the first season was episodic just to get the episodic stuff out of the way, and do all the "science fiction stories" that everyone would expect a sci-fi series to do, before getting into the arcs. And Crusade was even started that way, except that those stories were designed to be "seeds" for story arcs.
If anything, with
Crusade, I suspect that JMS was playing with the well-known, real-world history of B5 -- leaving the audience off-balance enough to discard any preconceived expectations based around its predecessor.
I think the case of
Excalibur going renegade would have been very different than the events of B5. In the earlier series, we ended up with what amounted to a full-blown civil war -- one side that had evidence that the government was not legitimate and was violating its own charter, and therefore brought it down. Lots of people joined the opposition, including large segments of the military.
The other dynamic that is different from B5 is that we know from that series' future-flashforwards that
Excalibur apparently does indeed find the cure. So while the crew is guilty of acting against orders, they are also heroes, and couldn't be branded public enemies as easily as the opponents of Clark were. (Even there, the Clark propaganda-machine was careful not to paint war-hero John Sheridan as a villain, only as a misguided man under the influence of aliens and genuine human traitors.)
The presumably-legitimate Earth government of 2267-78, most of which would know nothing about the secret Shadowtech work, would therefore be even more reluctant to launch a full-scale attack on the people who saved Earth's population from certain death.
The whole thing could have been very, very interesting.