I dunno, for me I thought it made a lot of sense from Worf's point of view. It really hit home Kurn's point about how domesticated Worf had become and how he had really accepted human morality along with his Klingon beliefs and the two conflicted inside of him.
It's not like we haven't seen Starfleet people erase people's memories with or without consent before in any other series. Either way Kurn dying in this episode would have been predictable and bland. It's what I liked about DS9, they were willing to shake things up and take chances. It couldn't always turn out great, but it showed they were trying.