Isn't that sort of the point? The Edelgard ending is the best result long-term for Fodlan, assuming she actually does successfully deal with TWSITD, but the question is whether the horrible deeds and incredible suffering it took to get there were worth it.
In the BL and GD endings, peace and prosperity is achieved in the epilogue but the systemic problems still exist because their leaders aren't willing to go to the same ends as Edel. Both Dimitri and Claude make strides in dealing with those problems during their rule, but it's unclear if the slow-and-steady approach will ever truly work with the church still in tact.
Edelgard believes it will not and that's why she thinks her way is the only option. Dimitri believes the people (commoners and nobles, Duscar and Faerghus, etc) need to be actively involved in determining their future together and that's why he takes a inclusive reformist approach vs. Edel's revolutionary dictator approach.
IMO it's up to the players to decide if the ends justify the means or not.