By Corollary $2.10$ in http://arxiv.org/pdf/0811.1955.pdf
Let $f:\mathcal{X}\rightarrow \mathcal{Y}$ be a proper morphism of Deligne-Mumford stacks and $\mathcal{F}\in D^+_c(\mathcal{X})$, $\mathcal{G}\in D^+(\mathcal{Y})$. The the morphsim
$$Rf_{*}R\mathcal{H}om_{\mathcal{X}}(\mathcal{F},f^{!}\mathcal{G})\rightarrow R\mathcal{H}om_{\mathcal{X}}(Rf_{*}\mathcal{F},Rf_{*}f^{!}\mathcal{G})\rightarrow R\mathcal{H}om_{\mathcal{Y}}(Rf_{*}\mathcal{F},\mathcal{G}).$$
is an isomorphism.
If $f:\mathcal{X}\rightarrow \mathcal{Y}$ is a representable finite étale morphism of noetherian algebraic stacks, then the functor $f^{!}$ is the same as $f^{*}$. Therefore we have an isomorphism
$$Rf_{*}R\mathcal{H}om_{\mathcal{X}}(\mathcal{F},f^{*}\mathcal{G})\rightarrow R\mathcal{H}om_{\mathcal{X}}(Rf_{*}\mathcal{F},Rf_{*}f^{*}\mathcal{G})\rightarrow R\mathcal{H}om_{\mathcal{Y}}(Rf_{*}\mathcal{F},\mathcal{G}).$$
Finally, $f$ finite implies $R^if_*\mathcal{F} = 0$ for $i\geq 1$. Therefore, if $\mathcal{H}om_{\mathcal{X}}(\mathcal{F},f^{*}\mathcal{G}) = 0$ we get
$$f_{*}\mathcal{E}xt^{1}_{\mathcal{X}}(\mathcal{F},f^{*}\mathcal{G})\cong \mathcal{E}xt^{1}_{\mathcal{Y}}(f_{*}\mathcal{F},\mathcal{G}).$$