Infections do not have have the ability to choose to not damage their host. People do have that choice, and many make it.
You are, I think, making a mistake that many people do, in thinking humans should have zero impact on the environment. This is nonsense. Does any other animal have zero impact on the environment? Beavers and wild boars can change entire watersheds! An ecologically aware future is not one where humanity has disappeared, merely one where we have consciously limited our effects on it. Ask a virus to do that.
No? If I ACTUALLY wanted to ride out through some sort of apocalypse, a bunker ain't gonna cut it. I would bankroll and actively participate in a fully self-sustaining off-the-grid community. Rich people always forget the second part, probably because they are psychopaths. Remember that article where they were asking about putting shock collars on their bunker security guys? If they literally just got beers with them once a week, they'd probably shoot all the migrants you ask them to. It's an irony that they consider their time 'too valuable' for that, as it turns out that the one thing you can't buy is a sense of community.
Of course, I would endeavor to not own several billion dollars of stolen property in the first place, but different strokes.