It was Rotian who killed them. Cyrus's family has history with Caelestialis, Cyrus's Grandfather having a similar experience with willingly Disc hunting for him. There's a symbol used by Cae to "mark" his underlings, typically given as a charm or a wall plaque. The one Cyrus's grandfather was given turned into a regular heirloom when he retired, and communication with Cae was severed. It was given to Cyrus's parents, which ended up being displayed on the side of their house.

Rotian and Cae have a history, as some people know, and at this point there was mutual hatred between them. Rotian as a whole despised the influence Cae had on others, going about breaking that in all the wrong ways. He killed anyone suspected of being connected to Cae, both Disc and Human alike. He saw Cae's symbol outside the house by chance and, lacking the context, killed whoever was inside. Cyrus and Melody came home as Rotian was still inside, which led to Cyrus's big scar.

It was mainly a big unlucky coincidence for Cyrus's parents, and the perfect opportunity for Cae.