He kills hundreds of soldiers, human and alien, who are only following orders, mostly unwillingly, from superiors who are only trying to protect their species and work for the greater good. He is given a chance to surrender to the HECU marines, but doesn’t, and keeps on killing. He makes a deal with the devil to escape an accident that may have been partially his fault. He murders Breen, who is simply a figurehead bureaucrat who seems to have good intention for humanity, even if he is a little misguided, and has not directly hurt anyone.
I’m not saying that Freeman is a bad guy, he’s just not a total hero sometimes.
“Tell me, Dr. Freeman, if you can. You have destroyed so much. What is it, exactly, that you have created? Can you name even one thing? I thought not.”