I like Serena said:
The formula $V=W/q$ is not generally true.
It only holds if the charge $q$ is small enough so it has no significant effect on the electric field.
In other words, $q$ has to be infinitely small, or really $dq$.
I do not have Griffiths', but does he perchance mention this?
To elaborate, a possible derivation is:
$$W= F s = (q E) s = q (E s) = q V$$
This derivation holds (only) if $q$ is infinitely small and if $F$ can assumed to be constant.
Right. Griffiths derives $W=qV$ in the context of one particle of charge $q$ in the presence of an electric field $\mathbf{E}$ that is not, itself, altered by the charge $q$. The field $\mathbf{E}$ is not assumed constant. I will type up Griffiths' derivation here:
Suppose you have a stationary configuration of source charges, and you want to move a test charge $Q$ from point $\mathbf{a}$ to points $\mathbf{b}$. Question: How much work will you have to do? At any point along the path, the electric force on $Q$ is $\mathbf{F}=Q\mathbf{E}$; the force you must exert, in opposition to this electrical force, is $-Q\mathbf{E}$. (If the sign bothers you, think about lifting a brick; gravity exerts a force $mg$ downward, but you exert a force $mg$ upward. Of course, you could apply an even greater force - then the brick would accelerate, and part of your effort would be "wasted" generating kinetic energy. What we're interested in here is the minimum force you must exert to do the job.) The work you do is therefore
$$W= \int_{ \mathbf{a}}^{ \mathbf{b}} \mathbf{F} \cdot d\mathbf{l}
=-Q \int_{ \mathbf{a}}^{ \mathbf{b}} \mathbf{E} \cdot d\mathbf{l}
=Q[V( \mathbf{b})-V( \mathbf{a})].$$
Notice that the answer is independent of the path you take from $\mathbf{a}$ to $\mathbf{b}$; in mechanics, then, we would call the electrostatic force "conservative." Dividing through by $Q$, we have
$$V(\mathbf{b})-V( \mathbf{a})= \frac{W}{Q}. \qquad \qquad \qquad (2.38)$$
In other words, the potential difference between points $\mathbf{a}$ and $\mathbf{b}$ is equal to the work per unit charge required to carry a particle from $\mathbf{a}$ to $\mathbf{b}$.
Then, in deriving $W= \displaystyle \frac{CV^{2}}{2}$, Griffiths writes as follows:
To "charge up" a capacitor, you have to remove electrons from the positive plate and carry them to the negative plate. In doing so, you fight against the electric field, which is pulling them back toward the positive conductor and pushing them away from the negative one. How much work does it take, then, to charge the capacitor up to a final amount $Q$? Suppose that at some intermediate stage in the process the charge on the positive plate is $q$, so that the potential difference is $q/C$. According to Eq. 2.38, the work you must do to transport the next piece of charge, $dq$, is
$$dW= \left( \frac{q}{C} \right) dq.$$
The total work necessary, then, to go from $q=0$ to $q=Q$, is
$$W= \int_{0}^{Q} \left( \frac{q}{C} \right) dq= \frac{1}{2} \frac{Q^{2}}{C},$$
or, since $Q=CV,$
$$W= \frac{1}{2} CV^{2},$$
where $V$ is the final potential of the capacitor.
It's this second derivation that I am questioning.