This is...ehh I don't mean to be a dick, but no.
This argument hinges on the idea that when the Emperor, the Black Templar, Astartes in general, Malcador, etc talk about humanity/mankind, that they're talking about people.
They're not talking about people, they don't give a SHIT about people as individuals, hence why most people within the Imperium have a horrific quality of life.
Like this premise is predicated on the idea that just because the ruling class of the Imperium talk endlessly about humanity, it means they adhere to humanist principles and they absolutely do not lol
It's why every baseline life is seen as having no intrinsic value beyond existing as the disposable tinder used to feed the flames of what they're actually talking about: The continued survival of the species by any means necessary.
"Humanity" to them is a vague general abstract concept, it's not about people.
It's similar to how the Third Reich talked endlessly about the German people, but were really just talking about the state. The actual individual citizens of Germany--and I'm talking about "Aryan" citizens, who had the best quality of life available--had a pretty shit existence under Hitler. You are nothing, you simply exist to serve the interests of the eternal war machine.
The Imperium is the platonic ideal of a fascist state. The Emperor is not a Secular Humanist, he's a fascist. It's pretty clear cut.
And the Black Templar would not kill racists and homophobes and miscellaneous bigots. I'm sorry, that's absurd. We know this because bigotry is rampant and extremely normalized in the Imperium, even if it doesn't look like modern day iterations of bigotry.
Abhumans are treated as second class citizens despite still being human. People who end up mutants through no fault of their own are hunted and killed, despite still being human. Psykers are vilified and thrown onto nightmarish Black Ships, despite being human. The poor are regarded as barely sentient trash, despite being human and the vast majority of the citizenry.
I mean, fuck, slavery is everywhere in the Imperium. There are child slaves.
If the Black Templar were as invested in the welfare of human life as you perceive it, they'd be outraged by such blatant cruelty and injustice towards members of humanity
But they aren't, because they don't give a shit. If they encountered a guy calling someone the f-slur, it'd probably register as a weird archaic form of bigotry, but they wouldn't do anything about it because it has nothing to do with their goals and values. They'd be as blandly indifferent to that as they are to all of the other varieties of bigotry and cruelty that exist within the Imperium in the 30th to 40th millenniums. That shit's all incidental.
Like come on, be for real. There's a good reason people are making 1:1 comparisons between the Imperium and real world fascist states. They are not dumb for doing that.