I think so (even in dimension higher than 2, assuming that $F$ and $G$ are still finite sets, and not codimension two subvarieties of course). Let H$H$ be an ample divisor in X$X$ avoiding F$F$ and let H'$H'$ be its strict transform in Y$Y$. Then H'$H'$ is ample in Y$Y$. In particular $Y={\rm Proj}(Y,H')={\rm Proj}(X,H)=X$.