After Sanakya's soul went into a slumber immediately the dungeon started to consume the remaining portion of her soul. Rein immediately tried to stop it but he was unable to do anything as the dungeon really had an upper hand after taking control over the majority of her soul.
Just as the dungeon took over 90 percent of Sanakya's soul, Rein immediately took action and destroyed her soul. Rein bit grinded his teeth together in frustration. He was not given enough time to come up with a solution to Sanakya's corrupted soul and he was forced to kill her to grant her last wish.
Sanakya wanted to die before completely becoming a puppet of the dungeon. She had not expected that telling Rein about the information would be so taxing for her, so much so that she fell into a slumber and lost control over her soul. So Rein did not want Sanakya to go to rest with regrets. So he was basically forced to kill her before the dungeon took over her soul completely.