Not quite the same thing, although I appreciate the analogy.
I'd agree; we do have an element of programming within ourselves due to the environment and circumstances of our upbringing, and that's a hard bit of coding to crack and/or change, but here, we're talking about a literal plan as something that has already been decided, rather than something that'll likely take place because of who/what the subject is.
Think on fate or destiny; if such a thing is real (I don't believe it is) but if it is, then somewhere, somehow, something has already decided that an event will take place in order for our destiny to be fulfilled. That would be hard coded into the fabric of the universe. We'd have no control over that as it was always going to happen.
What you're talking about with the programming is our learning, rather than our simply following an already predetermined path. Maybe someone/thing did write existence out in some format, and I was always supposed to type the words I believe in free will and my life is my own - ultimately we'll never know, but they are two very different concepts. One gives us an element of choice within existing programming and/or confinements. The other gives us nothing, except we think it does because we simply aren't aware that we don't have free will.
And that literal plan would be "God's plan" in this world. Loki's story is not analogizing anything that Christians don't think in mass right now. In fact... that something like 70% of the world believes right now.
In Christianity as well as in Loki, this thought about predetermination is a metaphor (not the same... but analogous to) for how so many of our actions seem to be habitual and predictable. Just like the Homer's Odyssey isn't the same as a man searching for meaning in his middle age... but it's analogous to it... it speaks to the same feelings, and it aims to teach us something about ourselves.
Also, we're not talking about these three time keepers "deciding" how things end up. For all we know, they chose one time strand because it was the only good option, and now they are sticking to that one, regardless of how what happens. The Diests had this same exact thought, that God created the clock...wound it, and let it go naturally from there. It's nothing new.
Again, you can ignore it away, but I'm going to give you the same answer: there's a difference between knowing what will happen and actually doing the thing. Many many many stories and fiction and even religions have played with this very concept. It's not new at all.
Basically, it sounds like you have a gripe with modern religion, and since you see this as analogous, you have a problem with this too. But have some humility. You don't need to agree with Marvel. All you have to do is adopt this as a modern trope in fiction for a reason. you call it lazy, but it's honestly more iconic.... this story is bound to be told, over and over and over again. The philosophical dilemma of predetermination is nothing new....not by a long shot... but it IS timeless. I'm sorry you have a personal issue with those kind of stories, but they exist for a reason, (to be a metaphor for our own lives) and time has shown that they can be insightful, entertaining, etc.
Like.... this isn't about your philosophical beliefs. If Marvel came out with a higher power that demonstrated a striking similarity to Brahman... I might be like... "gee, I don't agree with that, because clearly there needs to be a sacrifice for our sins ala Jesus." but that wouldn't stop me from accepting Marvel's right to make it's own storyline, and that I can still enjoy a story even though I share philosophical differences with it.