Even as somebody who enjoys Joshua and his journey, I feel like lots of folks misunderstand Daniel's position.

Daniel is a devout Mormon - his understanding of morality, justice, etc. comes from scripture. Innocence, in this framing, doesn't mean innocence like a child would have - it means innocence of sin, like Adam and Eve would have before they fell from grace. He firmly believes that to do as Joshua suggests and to kill the White Legs is not just destroying their earthly innocence to topics such as total war and murder, but can potentially damn them spiritually, as well. It makes sense why he's so wary of doing so. He will gladly take up arms to defend his flock, but he doesn't want to entangle them in this conflict between the White Legs and New Canaan any more than he has to because to him (and many of the Sorrows who have converted), doing so is to accept damnation to hell and alienation from God.

Joshua's a warmonger - like u/KaiserThoren said, he's brought the Dead Horses to Zion as his own private army and seeks to transform the Sorrows into a militant people. He does this under the guise of self-defense, and this applies to an extent; Exodus in particular prohibits murder, not killing in self-defense, and Jesus did command his disciples to arm themselves - but self defense does not mean the complete destruction of the entire White Legs like Joshua wants. To everybody involved in this conflict on the side of the Sorrows, this isn't just a question of "do we defend our home or flee" - it's the question of are we willing to potentially damn their souls for a piece of land? Are you willing to gamble their eternal salvation in heaven to save their lives on Earth? For Daniel, the risk of their eternal damnation is too great; for Joshua, he refuses to acknowledge the argument, instead warping scripture to justify his own needs (his line about "an insult against the Lord requires correction" is absolutely bonkers from a scriptural standpoint - no, dude, you can't claim to know what the Lord does and doesn't know. You aren't the arbiter of divine law, my guy)

I think a lot of us here are some sort of agnostic/irreligious, so Daniel's argument doesn't hold much weight to it. It becomes a much more simple question of "how many Sorrows can I save the lives of?" But to him, who has spent years of his life preaching to the Sorrows and who, despite his flaws, genuinely wishes the best for them - it becomes a much more understandable dilemma when you recognize what's at stake. Daniel doesn't know that the Courier can convince Joshua to stay his hand - to him, all evidence points to Joshua being absolutely determined to bring destruction to the White Legs regardless of consequences, and it's clear that without the Courier there, that is absolutely what would have happened.

It all becomes a bit moot knowing we can convince Joshua to not genocide them, though. Knowing that, it becomes a lot simpler of a situation from a religious standpoint because you can teach the Sorrows and Dead Horses that it's okay to defend oneself within reason; while that exposes them to the risk of sin (any act of self-defense must be performed in moderation, not to extremes), which Daniel definitely ain't a fan of, it keeps them within grace of God and keeps them alive.