"You can disable them entirely at game start, completely skip military tech, and your pollution cloud will still blight the land, poisoning trees and lakes (and fish) around you."You can turn off pollution too.
There are also mods that'll let you grow trees or fight pollution in other ways.
There's a cost to pollution in the vanilla game, when both pollution and biters are turned on, so it's not like this game is pro-pollution.
I have a bigger problem with nuclear waste having no consequences.
But even then... it's just a game!
I find it curious that some people get up in arms over the ethical issues in a game like Factorio, yet hardly anyone (outside the religious right) complains in all the violence in the most popular games of all: AAA first-person-shooters... or most games, really, as most of them place the player in the role of a killer, where you solve problems and win by learning to be a more effective killer.