The Crystal Gems wished to live in peace free from the persecutions of Homeworld's people. No such thing as a selfless wish.

Every one of those monsters the remaining Crystals fight and bubble were once a loyal teammate, either to Rose Quartz or to Homeworld. That's all been rendered beyond moot, and many of them became the monsters they wished to vanquish. Homeworld is operating by an order whereas the Crystal Gems seem to have some law of cycles in mind. Like how every great empire has followed almost the exact same patterns and phenomena from birth to decay.

You really have to forego a lot of morality and even some human empathy to actually personally sympathize with the Crystal Gems. It's all a matter of perspective, even Homeworld presents both its fair and unjust aspects. You could argue there's more pride in Homeworld's Gems with a more genuine sense of loyalty and servitude - Rose Quartz was trying to be a one-Gem revolution and all but four paid with their lives to side with her. How is that fair or just? That is how a human would address this issue. But a Gem, which cannot ever truly be like the human, would never stoop to such weak-minded approach.