Depending on your POV, each faction is motivated by "good" intentions. Zoraida and the Neverborn want to prevent the destruction of their world from the humans, the Arcanists want fair work conditions in the mines, the Gremlins are insane, but the Guild is the law. From a classical perspective, the Guild are the law makers and the peace keepers. Perdita and the Ortegas are in Latigo to defend humanity from the Nephilim threat. Lady Justice and her Death Marshalls pit themselves against Death itself in the Resurectionists. Sonnia and Samael protect Malifaux from the lawless destruction of the Arcanist, and so on.
One of the things I like about Malifaux is that no faction is always the good guy and no faction is motivated by unrealistic evil. Rather the story is more 'real' in that each character does their best to do what they believe is right rather than one faction just wanting to destroy, conquer or consume.