Master Chief would win. If you read the books, you will find that Spartan 117 of Jon, has no problems with killing women if required. The only thing that matters is the mission, and failure is simply not an option. The only way that Samus has an edge over him, is because her weapons are integrated into her armor. However with the improvements made to the Mark V Mjolnir armor, he is physically capable of moving at speeds that allow him to dodge plasma shots.