I agree with Phee that Amara has already lived well beyond the day she should haves died, and you can only defy fate for so long in fairytales. She was granted another century of life, but from what little we’ve seen so far, she squandered it by choosing destruction rather than mercy. She became an evil sorceress who had a merchant boy killed by Jafar and showed no sense of regret. If Amara had been shown to use her powers for good, rather than for evil, then I’d be sad to see her go, but she showed no mercy to her fellow townspeople so I don’t think she deserves to be shown mercy by Nyx. In fact, I think Amara sacrificing herself to free her two remaining sons from the bondage of their genie bottles would be the only real way for her to make atonement or recompense at this stage.
It’s very Rumple-like. And to extend the parallel I suppose that makes Cyrus a bit like Balefire–only in reverse. Nealfire decided to let fate play out with Emma and the Curse; Cyrus interfered with fate and look at all the bad things that happened.