A lot of people have been saying that either Wanda will now rebel against Stanley (to gain the Hammer and greater power) or that Stanley will put down Wanda (maybe even disbanding her) to gain the Pliers and affirm his belief that he should have all the tools.

None of that makes a lot of tactical sense. Stanley is a powerful warlord, even more so with the Hammer, and can pop/tame dwagons. He is an immense asset to any side (provided his ego is kept in check by good advisors/warlords). Wanda is a powerful caster, even more so with the Pliers, and can decrypt fallen units (making them, in many ways, as strong as ever). She is an immense asset to any side (provided she is not given completely free reign, and is balanced by more people-oriented allies).

If Stanley kills/disbands Wanda (or takes the Pliers from her somehow) then he loses one of his most powerful units (maybe his most powerful) as well as an intelligent advisor and commander. Plus, he loses the power of the Pliers; it's almost certain that he can't wield both at once, and that he won't attune to the Pliers. Getting rid of Wanda robs him of her utility as a caster, advisor, commander, and Tool.

If Wanda kills/overthrows Stanley (or takes the Hammer from him somehow) then she loses one of her most powerful combat units (maybe her most powerful) as well as a good commander and sizable leadership bonus. (Yes, Stanley is a good commander - that's how he rose in the ranks and became a warlord, then chief warlord, then found the pliers - just not a good overlord). Plus, she loses the power of the Hammer; it's almost certain that she can't wield both at once either, and that she won't attune to the Hammer. Getting rid of Stanley robs her of his utility as a fighter, warlord, easily-manipulated overlord, and Tool.

In either case, the side is stronger and more likely to achieve Wanda's/Stanley's goals if they work together, each with his/her own Tool.