Everyone loves these things, so lets try to put alignments on the factions.
Cygnar: Lawful Good - They are like an IK version of America, being world police.
Menoth: Neutral Evil - They only care about spreading their religion and will stop at nothing to do so.
Khador: Lawful Evil - They believe the territory is theirs by law, and are taking it back.
Cryx: Chaotic Evil - Need I say more?
Mercs: True Neutral - This could vary based on which contract you are talking about. Magnus's Agenda would be either Chaotic Good or Chaotic Neutral
Ret - Idk their fluff very well.
Trollbloods: Neutral Good - They are defending their homes and famlies from the various warring factions.
Circle: Lawful Neutral - They are trying to maintain the balance.
Skorne: Neutral Evil - They get a chance to loot and plunder if they invade Cygnar. They torture and mutilate their warbeasts.
Leigion: Chaotic Evil - Idk their fluff that well, but spawning vessels are neutral at best.