Ok, now I'm finally sure that you're not just using GW universe with some name changed, as in GW universe the Space marines that conquered most of the galaxy were already xenophobes killing any xenos race they encountered for the "good" of mankind superiority.
And even human colonies were not free from their wrath if they didn't submit at once to the great Emperor.
So yes indeed, your universe is nothing like that at all, I a like yours more as it still have some decency and a sliver of hope. ;)
Well not all of the marines are jerks. In fact it is stated that the wolves are one of the few nice...ish group. If you are human anyways. They did oppose the Grey Knights when they were about to do their whole execute mass numbers of guardsmen who may have even heard of them.
You should have seen them
I wouldn't be surprised if that old man was a psychic echo of The Emperor himself. If he ever got up of his Golden Throne He probably wouldn't be pleased of what has been made of the Imperium he worked so hard to create...
Son of Johnson
If one would want to be correct, it would have to be "Son of John", because that is exactly what Johnson says. You pretty much wrote there: "Son of John's son". Except that is, what you wanted to write.
It's worth mentioning that the Salamanders are nice guy space marines, read the stuff re the 3rd war for Armageddon. The Ultramarines created a mini empire where the standard of living is actually decent - in the grimdark this is no mean feat, Individual marines such as Pedro 'carry a mother and children to safety' Kantor are moral, and then you have the chaptors like the Raptors who care about their objectives, not personal glory. There are good guys in the grimdark, just overall the factions tend to be evil in their ways.
And the Space Wolves and the Inquisition don't get along because Logan Grimnar vociferously objected to the Armageddon Purge on moral grounds, and got away with it because he had the entire 15,000-strong chapter at his back.
There's PLENTY of decent and outright heroically good people in 40k, the setting just drowns them out. I like the author's version better.
Final thoughts: In the words of Matt Stover in the afterword to the Revenge of the Sith novelization:
"The dark is generous, and it is patient, and it always wins - but in the heart of its strength lies weakness: one lone candle is enough to hold it back.
"Love is more than a candle.
"Love can ignite the stars."
In the game fluff, the inquisition hates everything they cannot control, and the space wolves is a pain in their ass from milennia. The problem is not only the twelve great companies on their own, but all the relations they have that they dont even know.