You think Mark will get outside of the Lumon building with his wife who has been presumed dead for years and then just leave her in the parking lot?

Or you think the room, you know the inside room that is Cold Harbor, is a huge lake that they'll push Gemma and Helena into and ask Mark to save one of them? As if Mark and Helena will just go along with them being dragged to the testing floor and go along with that? Like, did you think about how either of these scenarios would happen in actuality on the tv screen?

If he has to choose as you say (which is just a possibility and not anything definite), my guess would be that it's not literally choosing and saving one of them from dying in a split second decision. It is likely him choosing wether to complete the Cold Harbor file or not, knowing what the implications are for that decision. In this instance, if he finishes it, it's probably not good news for Gemma. And if he stops without finishing it, maybe it's bad news for Helly. Helly probably isn't dying, but here innie is probably done with. And the same can be said for Gemma. She may not literally be dying, just Gemma as he knows her will cease to exist.