No, ths is not true. Let $E$ be a finite group and let $\phi:F_\Sigma\to E$ be a surjective group homomorphism. Let $A,B\subset E$ any subgroups and let $G=\phi^{-1}(A)$ and $H=\phi^{-1}(B)$. If $GH=HG$ holds, then by applying $\phi$ we get $AB=BA$. So if the claim was true, then for every pair of subgroups $A,B$ of any finite group we would have $AB=BA$. Now it's easy to find a counterexample.
No, ths is not true. Let $E$ be a finite group and let $\phi:F_\Sigma\to E$ be a surjective group homomorphism. Let $A,B\subset E$ any subgroups and let $G=\phi^{-1}(A)$ and $H=\phi^{-1}(B)$. If $GH=HG$ holds, then by applying $\phi$ we get $AB=BA$. So for every pair of subgroups $A,B$ of any finite group we have $AB=BA$. Now it's easy to find a counterexample.