From a narrative standpoint, Ra-den was killed to legitimize Ny'alotha and N'Zoth as imminent threats in a direct sense - showing the effect of Ra-den, a powerful figure we'd ideally come to sympathize with, being corrupted by N'Zoth's power and having us being forced to kill him because of it. I personally don't have much of an issue with Ra-den being killed off, and I think the story surrounding his sacrifice, corruption, and death was one of the high points of the 8.3.x storylines (notable in that most of 8.3.x was, well, seemingly hastily cobbled together and poorly executed).