The moral of so many "science gone wrong" stories is that some things should never be learned, discovered, explained, or created.

But is that really true? Well, as far as "created", that's a bit of a duh. Everything else? No! So many stories try to get these themes across, and while they can make some good points, often the invention itself is benign; even beneficial. It's more the means at which the invention was made that falls short of morality, and--more often than not--common sense.

I really think the idea of forbidden knowledge is more of a leftover from Lovecraftian horror stories (Which I personally loathe, as they teach us we should be afraid of the unexplained, and that the supernatural is inherently harmful or downright evil), which is really very anti-Christian to begin with. Wouldn't it be great to do the reverse as a Christian?

So... here are two things I want to see:

1. A story that explores the themes of trying to discover something, and why it's wrong to take immoral or unsafe shortcuts. Then the moral is more that there is more than one way to skin a cat. The truth will be there when you get there.

2. There are some things that really shouldn't be invented, done right. A story where the invention or creation might at first seem benign or beneficial from a shallow standpoint; but upon further examination isn't the best idea. I'd really love to see this done with an A.I. exploring the idea of why it's stupid to create truly intelligent software for the sole purpose of enslaving it, etc. Don't be stupid about it, though. Make a good point for both sides of why it should be made and why it shouldn't.

I think there are a lot of intrinsic assumptions to your arguments that are not as self-evident as you seem to assert. I'd also like to hear about some examples of the kinds of stories you refer to in each of your categories.

Why is it such a "duh" that there are some things that shouldn't be created?
What would the reverse of a Lovecraftian horror story look like? Teaching us to be fascinated with the unexplained?

You rig the question in #1, by asking why it would be wrong to take immoral or unsafe shortcuts. Probably because they are immoral and unsafe, is all that could be set on that. And what constitutes a shortcut?

I am not sure it is as self-evident as you seem to assert that it would be "stupid" to create an intelligent software for the purpose of enslaving it. And of course, it would be a good idea to write any story without "being stupid about it" but you haven't given any criteria for what makes a story "stupid about it" or how to make a story not "stupid about it."
Without clarification on some of these things, there can't really be much of a response to your post, because you more or less declared that you wished someone would write a story on a certain subject, from a certain viewpoint, without justifying the viewpoint or explaining what would make doing so "stupid."

You'll have to forgive me. I just got done with a really bad movie when I wrote this and it really ticked me off.

It's important to know the difference between doing something and doing something wrong. This is where many of these stories fall short. Let me give you an example.

In X story, Sam decided he wants to study black holes. So Sam builds a device to generate black holes for him to study. He creates a black hole, the story asserts via narration that there are some things man is not meant to know; it ignores the insane black hole device and jumps straight to the assertion that man was never meant to know about black holes.

This is only an example.

This is the standard formula for a science gone wrong story. I'd like for someone to write a story where A) The overall goal is not condemned but the reckless actions taken to get their are highlighted as a morality tale. Or B) The Creation itself is inherently flawed, not the means it took to get there.

Creating an intelligent being--as in, one capable of thinking for itself--only to force it to obey your every whim? I can only see good things coming from this. Slave rebellions never happen in real life.

Yeah, I wasn't vary clear about that Lovecraftian thing. But, basically, you got it: a story that teaches people to embrace and be fascinated by the unknown, where the villain isn't the strange and unexplained but a man or group whose fear of the unexplained might doom an innocent. I shouldn't have to tell y'all not to use a religious organization to do this. If anything, make the bad guys pseudoscientific "Philosophers", much like Lovecraft himself.

You know, E.T. kind-of follows this formula a bit... Huh. But I'd still like to see more of this. Better to do it without the cute alien anyways, as the message could kind of get lost. Have it be an unexplained phenomenon or some incredibly strange and alien creature. Something utterly strange: An alien that ultimately proves itself to be beautiful; not necessarily beneficial, though just beautiful in its own way. Beneficial does work, but it hammers the point too far into a preachy territory. Benign and beautiful has a more subtle a sensible feel to it, but that could just be my opinion.