I will =D

Second theory to implant -

If Mojang also wanted to make this semi-religious, the future theory could be true, but the evolution of mobs could be a lie.

Here are some other plausible reasons for what happened outruling evolution.

Ghasts:

These could merely be mutated forms of squids, as you stated above. However, there were other things that you did not account for.

Size - They could be covered in years worth of moon ashes
Flight - Assuming the fog IS moon dust wouldn't that explain why they can fly - they're virtually the same
weight as the atmosphere!
Fireballs - These are easily explainable. Squids like to swim, right? They swim in water near the core, but can
see outside the dust. They have control over a magma chamber directly in front of them, and can
make it spew out magma like a volcano at will by creating waves inside, which would also explain
why the ghast appears to "open up."

Zombie Pigmen:

These creatures are quite the odd concept to grasp. However, let's look at some scientific facts -

A virus or bacteria could never raise a corpse from the dead, as bacteria could not mutate fast enough to change to it's host's vital functionality, while a virus is technically not alive. They could only be created by:

FUNGUS

The fungus would initially spread into a miner by accidentally cutting himself on a fungus-covered rock underground while the world was still normal. It lay dormant until his death, at which point it made his body appear to vanish, by spewing out his soul and disguising itself as part of the rock. It then spread to take over the CNS (Central Nervous System) and took control over the body. The green appearance could be the fungus mutating to be able to eat the organs inside and then it would be very close to the surface of the host's skin, thus giving it the appearance of green skin.
The fungus would further mutate after realising that it's hosts deteriorating body could not last forever, and repaired the jaw, undisguised itself from the stone, and returned motor function to the body by repairing tendons and muscles that it devoured. It then began to hollow out the stomach, eating itself, while it looked for another host. It would then devour the host, which would pass into the empty stomach-like pit and be eaten by the fungus. Once the host is bitten, if he is not completely devoured, the fungus has spread into another host.
Perhaps all caves caved in when the sun went out and the moon crashed, spewing lava all over from the pressure, and wiping out all the miners. The zombies then found the next suitable host - pigs. Being used to bipeds for their capability, they used the fungus strains to turn it into a biped, ripping the skin in the process, which could be the reason for the hole in the head. They then found that gold was abundant, and took all of it to create (although very weak) weapons, as they found it killed their prey much faster.



Blaze:

Perhaps, at the end, the miner's souls flitted into the melting iron in a vain attempt to exist, before the rest of the iron was turned into quartz from the atoms re-organising from the force of the blast when the moon fell ( or perhaps, the Earth was blasted into the moon after the sun went out, which could account for the moon "turning red").
When their souls entered the iron, they burst their way out of the ground, creating the many caves, and found remaining fortresses that had been hidden far underground out of the miners' reach, having been previously made of Dark Matter beneath the void, but converted from the effort of the gravity. They then found to their delight, that they could defend themselves by expelling magma in a way very similar to the ghasts.


Magma Cubes:

I doubt they absorbed the rocks, as regular slimes die in lava. They were probably covered in the moon rock in a just-slightly-heavy-enough-and-just-slightly-thick-enough layer and then were covered in hot ash from the moon dust that was ignited by lava.
It slowly heated the moon dust on them, and they slowly adjusted to the heat, until they were completely covered. The ash eventually began to crack, and that explains for their molten lava-like core. Perhaps the slime shrank inside the ash, and that is the remains.

Wither Skeletons:

They're merely skeletons covered in cooled ashes when they couldn't get off the surface in time, and the Wither Effect comes from the ashes entering the entity's bloodstream.

Skeletons:

The lucky skeletons that weren't crushed underground. that explains why there's so few of them. Also, in the case of being skeletons, they could possibly be miner's souls that were too stubborn to leave their bodies behind and were consequently trapped inside. This could explain why they despise players, as they are perfectly normal, so they adapted to become hunters instead.

Goodness that's a lot to grasp...

You should do a blog series related to mythical creatures, just a suggestion :)

Just an update, I plan to make more mc theories, hopefully uploading them once a week (Lol we'll see how long that lasts). I also will keep uploading Steven Universe theories, because people really seem to enjoy that too. I may also make another blog series, but I have no idea what to do really :/