The approach you describe appeared in a recent answer of mine, so I'll explain what I meant a bit more thoroughly.
The typical statement of the divergence theorem in $\mathbb R^3$ goes as follows. Let $B$ be a simple (i.e. non self-intersecting) closed surface which is continuously differentiable (so it has a well-defined outward pointing normal vector $\hat n$ at each point). By the Jordan-Brouwer separation theorem, this surface is the boundary of a bounded, connected interior region $U$. Given a vector field $\mathbf F$ which is continuously differentiable on $U\cup B$, we have that
$$\int_B \big(\mathbf F \cdot \hat n\big) \mathrm dS = \int_U \mathrm{div}(\mathbf F) \mathrm dV\tag{$\star$}$$
Now consider the vector field $\mathbf F = \hat r/r^2$, with $B$ a simple closed surface enclosing the origin and $U$ the region enclosed. Naively, one might compute the divergence of $\mathbf F$ and find that $\mathrm{div}(\mathbf F)= 0$, suggesting that both sides of $(\star)$ vanish. However, this is not so, because $\mathbf F$ is not continuously differentiable (or indeed, even defined) at $r=0$.
As a result, $\mathbf F$ does not satisfy the requirements for the divergence theorem to apply. We could try to fix this problem by removing the origin from $U$ since $\mathbf F$ is continuously differentiable (with vanishing divergence) on $U-\{\mathbf 0\}$, but that still fails to satisfy the conditions of the divergence theorem because $U-\{\mathbf 0\}$ is not the interior of $B$.
This certainly resolves the apparent paradox - that $\mathrm{div}(\mathbf F)$ vanishes on the domain of $\mathbf F$ but the left-hand side of $(\star)$ does not - but it doesn't really tell us how to move forward with our analysis. We're doing physics here, and we'd like to talk about point charges after all. By extending the divergence theorem to include distribution-valued quantities, we can simply say that the divergence of the electric field due to a point charge is proportional to $\delta$, which matches nicely with the intuition from $\nabla \cdot \mathbf E \propto \rho$.