Losing atmosphere due to solar wind is very slow process. If you spent 10 millions years building the atmosphere, you can afford few millions years to build a replacement for that ship.
Yeah, but because of McGuffin it will happen in like 15 minutes if the super-villain gets his will. And then billions of Martians will needlessly die of suffocation and sun-burns. But our HERO John McLane III is there to valiantly save the day by employing fast one-liners and walking bare-footed on broken glass!!1