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The structural damage you inflict in Guerrilla is permanent, as noted in Destructive Savior on the main page. In the Origins film, a primary problem the Red Faction now faces as the rulers of Mars is a lack of efficient infrastructure. Now whose fault might that be?
That's not what infrastructure means. Infrastructure is the most basic framework of a system, not physical structure. It is most likely referring to the organization of the Red Faction, which worked well enough for a resistance group, but does not have the organizational capability to run the entire Mars colony as a government.
Don't know about you but when I went through I turned all those blue icons into scrap, and that included destroying pretty much everything of value in Dust, power plant, chem depo, Ark mine, etc. that is all infrastructure.
Alec Mason is able to smash down buildings with a sledgehammer because he's new to Mars. He grew up under Earth gravity, the buildings are designed to stand up in Martian gravity, which is a third of that of Earth. He is, literally, superhuman by martian standards.