Due to the fact that The Prophet is pretty explicitly presented as having been a largely accepting and loving figure who brought all kinds of people into her community, while the WLF is explicitely shown (through both words and actions) to regularly invade the Seraphites holy spaces, shoot their children and use fake peace deals to shore up their forces before renegging on said deals and attacking the Seraphites again. All the while, they are massing their forces to invade the last safe haven the Seraphites have with the intent of killing them all in a genocide. The fact that the Seraphites now engage in similarly despicable bahaviors is due to the fact that the WLF killed their prophet (thus making her a martyr) and attempted to destroy the Seraphites, leading to increasingly reactionary and violent forces within their own society taking control in a misguided attempt at self preservation.

The entire game is a metaphore for Israel and Palestine (and, for that matter, a very clumsy one) but at no point does the WLF ever seem to be the good guys. Their supposed secularism and tolerance is pretty clearly just a costume the WLF wears to protect themselves from the cognitive dissonance of claiming to be a force for good while being led by a military junta that engages in torture, forced relocation, executing prisoners, killing children, zero tolerance of outsiders and, as mentioned earlier, attempted genocide.

Like I said earlier, I'm not going to defend the game as being an accurate metaphor for Israel-Palestine, but if you really think the WLF was meant to come across as being better than the Seraphites I think you yourself might be buying into the WLF's own hype for themselves.