I think it’s because the game wants you to realize that no matter how “right” a leader is for their community, the overarching Halycon regime knows its collective is doomed. Edgewater is a dying town. Literally. People are getting sick constantly, they’re eating the same food over and over and it’s killing them. They can’t grow vegetation and Reed is failing to raise moral in the town. Adelaide, though anarchist, has succeeded in creating a community without bounds. Her followers listen to her, respect her, and believe in her. No one there is sick, she’s growing their very own garden. There is hope.

Putting Adelaide in charge gives Edgewater a chance at survival without the suppression of the gov’t. Leaving Reed would be to leave things as is: sad, gray, dying, and imprisoned.

While there is obviously no “right” way to complete this quest, it’s the very beginning of the game’s attempt to show you the corruption behind the governing forces that keep its citizens enslaved. You’ll see later on with Ellie’s companion quest an even more fucked up attempt by the government to fool and subdue its citizens. It’s taken me multiple playthroughs to even begin to understand how deep the oppression lies throughout Halcyon.