Void elves as part of the Alliance threw enemies into Void portals that took them to the worst places in the universe. A bit too late to set moral boundaries.
And I’m not saying the entire Alliance has to agree to this, but like you said it’s THE organization. Not everyone in it has to agree on everything. The foundation of new Horde was the ideals of Thrall, Cairne, and Vol’jin. The Honorable Horde. However, there were still cracks and misfits like the gladiator fights in Orgrimmar, Forsaken experiments, and the willfulness of the Warsong Clan. Alliance can still have its darker side without giving up what it stands for.