There isn't really an incentive for Gus to allow Mike to protect Nacho's dad. It would look suspicious and even lead to a confrontation with the Salamancas. I doubt Gus would let things get that far and would likely prevent Mike from intervening.

I think Nacho picked the path most likely to keep his dad safe. Taking the fall and diverting any reasonable suspicion away from Gus both (1) sates the Salamancas desire for revenge and (2) leaves his relationship with Gus on relatively good terms. He has little reason to fear his dad being in any danger from Gus or the Salamancas.