People are mad at the Crystal Gems for imprisoning Lapis Lazuli in her mirror, but it turns out they never did that!
In the episode, Pearl shows Steven the mirror, stating “We found this Gem powered mirror at the Galaxy Warp!”, meaning that they found Lapis in that state after the war.
Let’s connect this to another strange Gem phenomenon, Gem Shards. When a Gem becomes cracked, they lose sentience and become mindless Gem Shards that can be used to power various items. Gem Shards so far have been stated to not have a mind or consciousness, but simply act on instinct.
Now let’s go back to Lapis: When Steven reveals that Lapis is communicating coherently through the mirror, the Crystal Gems are absolutely horrified. Why? Because they thought Lapis was a Gem Shard. They thought her Gem was completely cracked all the way through, and she therefore didn’t have a mind to suffer through thousands of years of entrapment.
Pearl is the first to realize that a sentient being was trapped inside the mirror, even covering her mouth in shock.
Amethyst, showing an out-of-character moment of pure fear, urges Garnet to “do something”.
The Crystal Gems had no idea Lapis was still alive. They thought she was dead and were using her Gem to power the mirror. And they were utterly terrified when they realize that Lapis has essentially been tortured for thousands of years and they did nothing to stop it.
Now, why was Lapis put in the mirror? My theory is this:
During the war, Lapis was fatally injured with a blow to the back. The healer or doctor or whatever the Gem equivalent of a nurse is decided that she was too far gone to save her and wrote her off for dead, imprisoning her in the mirror because they thought she was dead anyway.
But she wasn’t dead, she was still alive the whole time.
This is why you always double-check before you bury a corpse, people.