If the choice is between cheaper housing with a longer commute, or expensive housing with shorter commute, it's completely unclear that the latter is more beneficial to humanity than the former, even if we only consider the number of deaths caused by each scenario. At the very least you haven't presented any evidence that this is so.
That is not the choice.
When people say that doing X has "negative value", they usually mean that it has negative value compared to not doing X, not compared to some imaginary solution that doesn't exist in reality.