Oh... boop. Something tells me the proverbial crap is about to hit the proverbial fan. All that's missing is the Ominous Latin Chanting.

A) Wanda would seem to be more powerful than anybody realized, except possibly Stanley.
B) Jillian is way too idealistic for her own good. She didn't even consider the possibility that Wanda could be working for Stanley of her own free will.
C) According to the rules we've been told about, the relationship of faction leader to subject is not one of magical compulsion per se; it's more like the natural laws of Erfworld. Whether units serve based on friendship, mutual goals, or money is irrelevant; they all have a Loyalty stat, among others.
D) Warlords and casters in particular seem able to make independent decisions. They are not slaves to their ruler's will and can change sides, disobey orders, or coerce other independent units to do the same.
E) Presumably, warlords and casters, upon the death or defeat of their faction's ruler, don't automatically disband like ordinary units, but rather may be captured, become mercenaries, or switch sides. I'm still not entirely clear on whether a designated heir is required for this or simply allows the side to continue existing after its ruler's defeat.

Based on the above, the simplest rational explanation is that, when Stanley captured FAQ, Wanda switched to his side of her own volition. Why she did so, and why she continues to remain loyal to him while his side is losing have not yet been revealed in the comic. Given what we've seen of Wanda's personality and motives, she could very well be even more evil than Stanley himself, but I think it's a bit early to pull out the Epileptic Trees just yet - we just don't know enough to speculate with any accuracy.