Giving your players moral decision points in a game is fine and can be a lot of fun.
However, I am reminded of the Survey in Dragon Magazine about 30 years ago that asked what kind of PC the players wanted to play and one of the choices was "In real life, I can trip over a garbage can. I want my dwarf to not have this type of thing happen to him.".
In other words, some people want to play heroes. Like real people, heroes are not infallible, however, some people want to play them as nearly infallible, larger than life. That's hard to do as a player since DND is not a novel. The author cannot just make it all work out in the end. If the DM presents a situation where the player has to decide between the PC's morals and the "greater good", it pretty much is a lose lose situation regardless of how the player decides. This is not always fun for all players.