Rick and Co have done far worse things than The Saviors, who, up until the conflict actually started, killed 6 (Denise, Abe, Glenn, Spencer, Olivia, Benjamin) people. In the same time frame, Rick not only stormed their compound for their own benefit (basically taking over The Saviors deal with Hilltop) and began murdering them in their sleep, and then Carol lured some in and burned them alive, and then she killed another five or six of them, all in all upwards of 30 people. All in all, Rick and Co have ZERO moral superiority over The Saviors. Keeping the prisoners is part of them coming out of this not just as victors, but having done it without becoming The Saviors. And now you know Jesus since this action defines his character. He doesn't want anymore people to die than have to die, and he knows you can't just win in this conflict, you have to win like the good guys. What's funny is when he said to Morgan "Once this is over, once we've won. Those who are left over, we have to live with them", is actually what Negan tells ol Rapey Dave in the comics before he kills him. By your own logic, Negan should have killed every single person in the line up, then should have went into Alexandria and burned it and everyone alive, for all the bad things Rick and Co did to his people, so they wouldn't retaliate like they are right now.