The answer is no. Before I explain why, let me reduce the problem to a problem in algebraic topology. Consider the natural map $Pic(X\times X)\stackrel{cycle}{\to} H_2(X\times X)\to End(H_1(X))$ where the second map sends a cycle $\sigma$ do the endomorphism $y\mapsto (\pi_2)_*(\pi_1^*y \cap \sigma)$.
For the divisor $D$ as in the question, the associated endomorphism is the map $f^*f_*=\sum_{g\in G} g: H_1(X)\to H_1(X)$. Hence, it is enough to find an example of a curve $X$ with an algebraic action of a group $G$ such that the sum of the elements of $G$ acts on $H_1$ by an endomorphism which is not divisible by $|G|$. Since every finite cover of an algebraic curve is algebraizable, this reduces the problem to a purely topological question about orientable surfaces.
Consider the example of a surface $M_3$ of genus 3. Let $C_2$ acts on it by rotation of $180^\circ$ around the middle hole (i.e. draw a torus with two handles and consider a rotation of the torus that interchange the handles). Then, as a representation of $C_2$, the first homology factors as $\mathbb{Z}^2 \oplus \mathbb{Z}[C_2]^2$, the first factors corresponds to the middle torus and the second to the two interchanged handles. Hence, it is enough to show that summation over the elements of $C_2$ on this module give rise to an endomorphism which is not divisible by $2$. But this is true already for $\mathbb{Z}[C_2]$, since the matrix
\begin{pmatrix}
1 & 1 \\
1 & 1
\end{pmatrix}
is not a multiple of $2$.