The so-called 'work'-Energy theorem is really an application of Newton's 2nd law, not a statement about work in general. Only in the special case of a point mass (or rigid body) is that "work" term really a work (in the conservation of energy sense).
If you take a net force acting on an object (like friction) and multiply it by the displacement of the object's center of mass, you get a quantity that looks like a work term but is better called pseudowork (or "center of mass" work)--what it determines is not the real work done on the object, but the change in the KE of the center of mass of the object. This is usually called the "Work-Energy" theorem:
F_{net}\Delta x_{cm}=\Delta (\frac{1}{2}m v_{cm}^2)
Despite the name, this is really a consequence of Newton's 2nd law, not a statement of energy conservation.