The Green's function will not always be symmetric.
The Green's function formalism really involves considering two problems,
## \mathbf{L}_\mathbf{x}u = f(\mathbf{x}) ##
and
## \mathbf{L}_\mathbf{x}^{\dagger} v = h(\mathbf{x}) ##,
where ## \mathbf{L_x} ## and its adjoint, ## \mathbf{L}^\dagger_{\mathbf{x}} ##, are differential operators. These operators will satisfy the generalized Green's identity
## \int \left[ v^{*} \mathbf{L_x} u - u \left( \mathbf{L}^{\dagger}_{\mathbf{x}}v \right)^{*} \right] d^3 x = ## term that vanishes only if ## \mathbf{L_x} = \mathbf{L}_\mathbf{x}^{\dagger} ##.
Let's assume that ## \mathbf{L_x} = \mathbf{L}_\mathbf{x}^{\dagger} ##, so that the right hand side really does vanish. Corresponding to the two problems we are trying to solve, there will be two different Green's functions, ## G(\mathbf{x},\mathbf{y}) ## and ## g(\mathbf{x},\mathbf{y}') ## that satisfy
## \mathbf{L}_\mathbf{x}G = \delta(\mathbf{x}-\mathbf{y}) ##
and
## \mathbf{L}_\mathbf{x}^{\dagger} g = \delta(\mathbf{x}-\mathbf{y}') ##.
If we set ## u = G(\mathbf{x},\mathbf{y}) ##, ## v = g(\mathbf{x},\mathbf{y}') ##, and put these into Green's identity (keeping the above two equations in mind), we get
## \int \left[ g^{*} \mathbf{L_x}G(\mathbf{x},\mathbf{y}) - G(\mathbf{x},\mathbf{y})\left( \mathbf{L}^{\dagger}_{\mathbf{x}}g(\mathbf{x},\mathbf{y}') \right)^{*} \right] d^3 x = \int \left[ g^{*}(\mathbf{x},\mathbf{y}') \delta(\mathbf{x}-\mathbf{y}) - G(\mathbf{x},\mathbf{y}) \delta(\mathbf{x} - \mathbf{y}') \right] d^3 x = 0##.
Evaluating the integral in the last equality gives
## g^{*}(\mathbf{y},\mathbf{y}')-G(\mathbf{y}',\mathbf{y}) = 0 ##,
so that
## g^{*}(\mathbf{y},\mathbf{y}') = G(\mathbf{y}',\mathbf{y}) ##.
Because we have assumed that ## \mathbf{L_x} = \mathbf{L}_\mathbf{x}^{\dagger} ##, we really have ## g(\mathbf{y},\mathbf{y}') = G(\mathbf{y},\mathbf{y}') ##, so that
## G^{*}(\mathbf{y},\mathbf{y}') = G(\mathbf{y}',\mathbf{y}) ##.
Finally, if the differential equations do not involve any complex coefficients, the complex conjugation will not change anything, and we will have
## G(\mathbf{y},\mathbf{y}') = G(\mathbf{y}',\mathbf{y}) ##.
So only if the differential operator ## \mathbf{L}_{\mathbf{x}} ## is equal to its own adjoint and has no complex coefficients will the Green's function be symmetric. On the other hand, this is the case in a wide variety of circumstances.