An interesting what-if.
Now, you can put in a kinda-sorta similar situation. Say, the War of the Rebellion happens, but it peters out instead of ending in Virus, and the damage isn’t as severe. Assume the war only goes on for five or seven years…
…and then, Emperor Lucan is assassinated by a sane Admiral who gets a broad armistice going. Even Strephon’s Stronghold survives: but while there is an end to the fighting, getting a proper peace agreement and a formal end to the war proves much more difficult, taking a few decades. The end result is a collection of large starnations, of roughly a sector or more in size.
Give them a century of independence. Squabbles continue, and some border strife, but there isn’t a major war.
Then, an outside threat comes up: perhaps a Solomani push coreward, or the Vargr go under one banner to go rimward, or the weak K’kree get a lot less weaker (say, a technological renaissance), but retain their hatred of meat-eaters… but are now in a position to do something about it.
So the divided princes of the Imperium get under one banner to fight the powerful threat: and they win!
But who did they gather under, and what happens now?