How can I prevent the untimely demise of John's wife?

There's a few videos on this page that go over the various endings. Although it's possible there's a perfect ending where everything is fine, I highly doubt it.

The entire game is a meditation on making tough choices - you can put aside your own happiness and needs in order to save the planet, or you can spend a few more hours with your family, thereby sacrificing everyone's future.

The game wants to put you in a terrible situation and make you think about how you'd choose. Feeling the effects of those choices is central to the experience. Having an ending where everything works out fine for everyone is kind of counter to the message the game is trying to send, so I find it highly unlikely that one exists.