No Mankind here are the bad guys.
They're the bad guys because when the Oretti, a peaceful species that got repeatedly invaded by everyone came to a Rouge Trader and offered her precious materials in exchange for a route to a safe system to flee to she took the offer then, following Imperial Doctrine, betrayed them and sent them to certain death.
They're the bad guys because when the Endymine Cordat came to them looking to coexist, offering them anti-daemon technology the Deathwatch invaded, drove them to the brink of extinction, Exterminatused their home world and left the survivors in a feudal state.
They're the bad guys because when they encounter a multi-species coalition with humans being part of it they're so disgusted they try to annihilate them on principal and enslave the surviving humans. More than once.
They're the bad guys because they go the extra mile to not only wipe out an ancient race of scholars but also grind their bones into dust, mix that dust with the crushed data crystals containing all their culture and knowledge and then shoot the mixture into the sun.
They're the bad guys because when they invaded the Keylekid expecting a tough fight and finding a race that abhored war and therefore regulated warfare under strict rules of engagement they responded by orbitally bombarding them.
They're the bad guys because when they encountered the Xenos of Carmyn a primitive race whose only high technology came from traders the Imperium fire bombed their world then went down to exterminate the stick and sling wielding survivors without mercy.
They're the bad guys because when they discovered the Sylvae, a race of low tech but high spirituality they bombed their centres of worship to annihilate their culture.
They're the bad guys because despite that when they encounter a race that does prey on human subjects they're totally willing to let it slide for the right benefits. https://wh40k.lexicanum.com/wiki/Skorl