I believe that what doesn't make those games controversial today, is the fact the points I rose are only parts of the games and I agree with you both.
I previously said that I disliked Zombies games, in fact I only don't play them, I don't hate them. Sure, when I talked about green blood, I was refering to the first House of the Dead which had its red blood censored turned to green.
In strategy games, I often use those tactics or strategies, sometimes in a roleplay sense, sometimes because I feel the game forces the player to use them; not using them often makes the game really much harder. I agree, sometimes those tactics have a further punishment, but sometimes it's the contrary.
I am thinking of another partial censorship, when I searched about the Uncharted Waters series, I found a story telling that the original Uncharted Waters 3 (on japanese Windows PC) had slavery. But a further patch removed it.
High Seas Trader didn't have slavery, but the developers themselves made a note about their choice in the end ot the manual. Although it made the game less roleplay because of choices of that era (even if the player wouldn't be forced tu use it), I respect their choice and the fact they clearly speaked about it.
In Europa Universalis 2, I usually don't use it but I understand that it's here and can be used. When I played an english long campaign, I often slay natives to stabilize my colonies though.
All in all, the thing that annoys me is the fact we clearly make a difference between controversial parts of a game and an overall controversial game because the later has poor other gameplay. I could understand that Hatred could be removed from greenlight because it doesn't add much beyond its controversial core. Because it lacks of everything else. But I don't understand that other games with some kind of similar controversial things only stay on store because they have other things, and the excuse to remove Hatred being "it's controversial". Saying "it's a poor game" would make me alright.