Okay so the fact you say 'fractured' is interesting, because abolishing the Imperium doesn't necessarily mean total every-sector-for-themselves, y'know? The Great Crusade basically tore apart every other hopeful new interstellar empire, good and bad, and, more to the point... the Imperium's already basically that fractured. That's what happens, constantly, where the Imperium misjudges a threat and then only turns around to meet it way after a easy resolution is possible. A galactic alliance of empires, each leading their own, smaller territories, that work together and maintain firm alliances, would by default be more stable than the Imperium's so called unified empire, just by dint of not being the Imperium.
you're making the assumption that they would be firm allies if they weren't a part of the same empire.
Furthermore if the imperium As a whole with its functionally bottomless pool of manpower will still struggle against a hive fleet how the hell is a colution of smaller empires which by the very definition of the term is less coordinated then a single bodied empire going to stop that?
further let's say Ork Raiders take over one of these empires and then target another. without a higher authority telling them to sectors that currently aren't under threat are not going to contribute resources to deal with that Ork incursion.
which means the targeted sector is going to get overrun which in turn means that the ork is going to escalate.
without a central system the news that hey this WAAAGH is building up steam is not likely to spread too far. And with each empire that is destroyed it gets larger and more powerful to the point that it's going to start swallowing multiple empires simultaneously. At that point what are you going to do? Because sure that orc looks really scary but you are currently dealing with pirates right now and you can't be bothered to go help someone that's very far away from you. So the people that are currently fighting that orc are fucked.
if left unchecked by a significantly more powerful entity that work is going to eventually conquer everything.
Now repeat that process for chaos and Nids .
because people are only interested in their self interest they are not going to go far out of their way to help someone else with what is their problem.
Hell let's look at badab for a second. The independent resource extraction grid was at one time one of the most resource rich sectors in the entire fucking galaxy. The carthago sector right next-door was the one that was in charge of distributing those resources across the galaxy. When the resource extraction grade was essentially being swarmed by Chaos forces Forks El Dara and I'll sorts of other things they didn't lift a finger they just sat there and did nothing. It required the High lords to place space Marines in that area for it to calm down.
if they wouldn't raise a finger to assist the people who were giving them mountains of super valuable materials what makes you think that sector b is going to help sector a for anything?
and all of this isn't even looking at the fact that there are threats out there that require the imperium to put its entire back into fighting in a united push. without a single unified command structure they have no fucking chance. Hell even with one they are looking up words at a shot in hell.
Yes and that has been the justification of every Hard man making Hard decisions (Usually while drinking hard and taking hard drugs because that is how the nobility rolls in 40K). 'There are worse things than us therefore the Super-Orwelian Hellscape we have made is justifiable, now shut up and eat your corpse starch.'
By all means tell the random hab dweller who just got shanked by his son for the windowless room barely high enough to stand in by his only son, because that is the only wealth he is going to have that all this is worth it because at least he did not get eaten by an alien.... you get eaten by your fellow man instead in the form of corpse starch. Tell the countless people who are burned alive in orgies of zeal and xenophobia that their death and torment is worth it because hey the Dark Eldar would have tortured you more artistically. Tell the entire peaceful alien civilizations some of which have never even seen a human before they are bombed into oblivion that their death is acceptable because some other aliens may have betrayed humans twenty thousand years ago at least according to ten thousand year old propaganda.
The IoM is evil, pure and simple, it was evil from its inception and it has only gotten worse since. I would say it should be wiped from history, but no because then it could not be held up as a standard for the most horrific excesses of tyranny that 'pragmatism' can lead one to.
it wasn't always supposed to be like that the imperium was a temporary measure created by the emperor to conquer the galaxy and deal with threats that we're going to conquer the galaxy and wipe out humanity and by extension everyone that isn't an orc or chaotic.
Hell papa Smurf didn't even get a chance to properly rework everything because he was gained in the middle of putting everything back together. And everything else has been trying to hold together for the past 10,000 years.
if you put a less brutal organization in this universe it will most likely be slaughtered. Seriously try putting the systems alliance in the 40 K universe and try to imagine them surviving this or the Federation from star treck and see how long they are methods last in the face of a Ork WAAAGH, Genesteelers, chaos cultists and all sorts of other Horrors.
You mock them and certainly there are aspects that deserve marking I'm not going to defend that. Nobility and worth from bloodlines is bullshit and not worth a damn outside of shit like Big E's bloodline of bullshit.
but tell me how exactly are you going to deal with people who worship a different God whom is a aspect of Khorne?
how do you politely deal with a gene Steeler infestation that is nearly impossible to neatly get rid of?
How do you stop chaos corruption?
there are 1,000,001 hard decisions in 40 K it doesn't excuse when people do stupid bullshit but in many cases there are good people who are forced to make shit decisions.
Cephas Cain is despite his own protestations over the fact as close to a hero as you get. he cares for his subordinates he puts his life on the line and he will regularly fight things that are so far beyond his weight class it's kind of hilarious.
but he still hast to make decisions like killing PDF whom are just following orders to prevent a war with the Tau. Him executing and killing people whom are loyal can be considered evil by the standards you're putting out. But if he didn't do that there would've been a war in the imperium would not have been able to deal with the Nids that were coming.
what would you have done in that situation diplomacy had failed and they were going to kill those diplomats if you don't kill them everything gets fucked but they don't deserve to be killed because they're just following orders and they are trying to defend their home.
The best stories in this universe are about people whom see that the universe is a shitty place and are trying to do the best they can in it. Save as many people as they can and do as much good as they can knowing full well that many of their actions can be considered evil by shifting the perspective just a little bit.
saying it's not worth defending is kind of spitting on the lives of countless trillions whom believe that yeah it is worth defending and they are willing to throw themselves at literal demons to do so.
If you want a happy ending in this universe you're going to have to fucking earn it going up a very steep hill but it makes it so much more rewarding when you do manage to flip off reality kick it between the legs and actually managed to save the day. You can't win every fight you can't be completely blameless but you can do the best you can.
this is not DC where the good guys always win. this is a universal were the bad guys quite often win. and who the bad guys can occasionally be rather gray but there is still good in it.
for every fat noble commander who sacrifices millions of men to achieve nothing more than to further his own career you have people who face impossible odds to save those around them.
TLDR: yes the system is fucked and needs a significant amount of cleaning and significant reworking streamlining and generally just making better. but it's not going to be a swift wave your hands and everything is better fix you have to earn everything because everything is trying to stop you from making the world a better place. So spit in it's face and do the best you can.