It shouldn't absolve them. None of the team has clean hands. Of the four who went in, Fitz was the only one who didn't fire a weapon, but he got them past doors, which he knew weren't being opened for parleying, and he carried and produced a flash-bang-type thing on request, which he knew wasn't just for show and which was used to create the opportunity to mortally wound one of the guards. Fitz is just as guilty as any of them. Coulson gave tactical orders and fired his weapon, and all four of them knew what they were doing. Coulson made it clear he feels remorse, and under his leadership, the team has appropriately acted so that the guards' sacrifice won't be in vain. Even if it turns out that two (or more) of Coulson's team were evil, it would be wrong for the rest of them to scapegoat the evil members and lay all the blame on the evil members' shoulders, for actions they all cooperated in carrying out.