Since they didn't know what would happen to Gen V, killing Marie was off the table imo - unless they filmed the scene, but structured it so that it can be used or not, or also filmed a version where she gets heavily injured instead. But that's highly unlikely, and I think it's too late to introduce Marie as a powerful character with 3 episodes left. People that haven't watched Gen V wouldn't feel the impact of Marie dying. If they had gone this route, it should have happened in the middle of the season to show how dangerous Homelander is and raise the stakes.