The show is an allegory for being trans and how family may treat you like shit for wanting different things than them. It is made for kids under 13 years old. Telling kids they should kill people after they have changed and agreed to fix what was broken seems like a bad thing.

Also, the creator (Rebecca Sugar) is a queer Jewish person, so I think they are well aware of the history of fascism and its consequences. They chose to make the tone and arc of the show anyways, and maybe you should think about why they made that choice before criticizing a children's show for not encouraging murder as a solution to problems.

Also, shattered gems are shown to still have at least some awareness, meaning that shattering the Diamonds wouldn't be killing them, but subjecting them to eternal torture. While also removing the only hope for fixing the gems that are corrupted. Which is what the Diamonds are tasked with to start making things right, along with giving up their social power over the rest of the gems.