I think there was a misunderstanding on some point.
First of all, the fact that the Mind Flayer is ultimately the big bad of ST doesn't in any way take away the human dimension of the story, on the contrary it strengthens it and brings a more original dimension.
It reinforces it in the sense that if you look at things with more finesse in a second reading plan, the Mind Flayer embodies through its actions on the human characters, a personified projection of the fears, of the psychological suffering which lies dormant in our unconscious.
He's the pivot point which will bring the human characters who are impacted by his actions, to express this human aspect, this human aspect laid bare which will face its trials by showing all its beauty just like all its horror.
He's a spotlight that will highlight humans, show their abilities to demonstrate bravery, strength, to grow, to show compassion from our heroes.
There is nothing problematic for the Mind Flayer about being the big bad in a human story, it's through the emotions of your human characters, their story, how you appeal to the public through them you will tell this human story.
It doesn't pass through its antagonism, but through its characters who live this adventure, with whom the audience identifies and feels this humanity in them which echoes theirs.
You tell a human story through the emotions that your human characters make you feel, through their trials and how they will react and come out of these trials, how it will impact them and finaly you, the public, what you feel inside in echo of your own humanity.
For Henry, yes he can be completely forced to do these things by the Mind Flayer.
As you can see in ST VR, the Mind Flayer distorts Henry's psychic reality.
Others have previously carried out relevant analyzes on this subject.
Which leads to something very insidious, a distortion of reality for Henry, in what he feels and experiences, what he wants, leading him to think he is in control
(to be able to better control him, what a perfect puppet is the one who is unaware that she is being controlled, no risk of resistance and rebellion),
making him believe that what he is doing is right, leading him into dead ends where he has no choice.
I use this example often, but it’s the one that sticks so well.
See Kylo Ren, Palpatine whispers, torments him since he was in his mother's womb ! All his life he has had dark thoughts, that he is a horrible person, that he hurts others, that no one likes him, etc...
At the beginning the character rejects his ideas, refuses to believe in them and attaches himself to the light.
But events caused by Palpatine will force him to believe his dark ideas, events which will isolate him and lead him to think that he can only be a bad person and that his place is in darkness.
You have a very similar pattern with Henry, his dark thoughts were perhaps already latent, but the Mind Flayer blew on him, blew on the embers intentionally to force him to do what he wants, to make him vulnerable too to his manipulations and make him think these horrible things.
The Mind Flayer clearly exhibits predatory behavior.
I am convinced that season 5 will show us since we will explore Henry's memories in the 80s, Henry's suffering for the loss, his sister in particular (someone pointed out that Holly's kidnapping was due to fact that he has not mourned, that he is in this delirium of taking her for his sister), that he never wanted that and that all of this is the work of the Mind Flayer who used this instability/weakness to manipulate him as he pleases.
In the scene where Henry scares his mother with the spiders you clearly see young Alice's foresight about this "you're not Henry".
that too, from a human point of view, is strong and resonates with many people.
Depression, autism, loneliness, abusive grooming, the dark side of the human spirit, etc...
It's in exaggerated form in the fictional framework of the show, but we clearly have these human aspects highlighted.
This goes back to what i was saying above, don't just see the Mind Flayer as "a monster/supernatural creature" but as a metaphor for the dark iceberg of the human psyche.
And that’s understandable.
It honestly has a lot more personality than a basic human, especially in a fantasy series !
I also think we have 2 plots to distinguish :
You actually have the human with all the political/military intrigue with the Russians in particular, but you also have the "magic" intrigue, the quest of the hero from the famous initiatory tale on El's side (with Will probably also in the S5 in view of what is teased about the character)
And with the DnD inspiration and many things relating to adventure in the show, to fantasy, you clearly have the hero's initiatory journey in addition to the human dimension.
But both complement each other anyway...
After all, isn't a hero defined by his human values ?