I think your confusion lies in the distinction between "," and ";", i.e. partial and covariant derivative. First of all, by the product rule, we have that
$$\delta\Gamma^{\alpha}_{\mu\nu}=\delta\bigg(\frac{1}{2}g^{\alpha\delta}(\partial_{\mu}g_{\nu\delta}+\partial_{\nu}g_{\mu\delta}-\partial_{\delta}g_{\mu\nu})\bigg)=-\frac{1}{2}h^{\alpha\delta}(\partial_{\mu}\overline{g}_{\nu\delta}+\partial_{\nu}\overline{g}_{\mu\delta}-\partial_{\delta}\overline{g}_{\mu\nu})+\frac{1}{2}\overline{g}^{\alpha\delta}(\partial_{\mu}h_{\nu\delta}+\partial_{\nu}h_{\mu\delta}-\partial_{\delta}h_{\mu\nu})=-\frac{1}{2}h^{\alpha\delta}(\overline{g}_{\nu\delta,\mu}+\overline{g}_{\mu\delta,\nu}-\overline{g}_{\mu\nu,\delta})+\frac{1}{2}\overline{g}^{\alpha\delta}(h_{\nu\delta,\mu}+h_{\mu\delta,\nu}-h_{\mu\nu,\delta})$$
Note that the linearization of $g$ with upper indices is $g^{\mu\nu}=\overline{g}^{\mu\nu}-h^{\mu\nu}$. This is where the initial minus come from. Next, observe that
$$\delta\Gamma^{\alpha}_{\mu\nu}=-\frac{1}{2}h^{\alpha\delta}(\partial_{\mu}\overline{g}_{\nu\delta}+\partial_{\nu}\overline{g}_{\mu\delta}-\partial_{\delta}\overline{g}_{\mu\nu})+\frac{1}{2}\overline{g}^{\alpha\delta}(\partial_{\mu}h_{\nu\delta}+\partial_{\nu}h_{\mu\delta}-\partial_{\delta}h_{\mu\nu})=\frac{1}{2}\overline{g}^{\alpha\delta}(\nabla_{\mu}h_{\nu\delta}+\nabla_{\nu}h_{\mu\delta}-\nabla_{\delta}h_{\mu\nu})=\frac{1}{2}\overline{g}^{\alpha\delta}(h_{\nu\delta;\mu}+h_{\mu\delta;\nu}-h_{\mu\nu;\delta})$$
where the covariant derivatives are with respect to the background metric $g$. To see the last to last equality, just spell out the terms $\nabla_{\mu}h_{\nu\delta}$ etc. explicitely using Christoffel symbols.