I find it interesting that you addressed Half Life 2: Episode 1 in your input on death in many games. However, the game addresses the protagonists’ view of this in itself, though indirectly. The only people subject to the hurling of bodies were the “Combine Overwatch,” the law inforcement of the distopian society. When one looks at an image seen on one of the walls of a station in the underground, which depicts a comparison between a chimpanzee, a human, and a human who had become a Combine Overwatch, notice the fact that the Combine are lacking a portion of their frontal lobe. At another point in the game, Alyx Vance, the lead female protagonist, shows sympathy for the, “Stalkers” another example of the Combine’s mutilation and forced labor.
Dispite the seemingly compassionate nature demonstrated by Alyx, which I take to be opinion of the game’s general public, she finds amusement in one of the Combine’s soldiers having been attacked by an alien parasite, saying, ” Its a Zombine, a Combine zombie! Get it?”
What I got out of the game is that the people of the Half-Life universe distance themselves from their enemy under the pretense that their identity has been taken away.
I’m not attempting to criticize your comment, since sending living, breathing things flying to their doom with repurposed lab equipment is still very morally questionable, but add to it. Valve addressed the ethical qualms of murdering these altered humans in a manner that effectively just distances it from the player, similar to your example of Pikmin.

Gee, now I must sound like some sort of fangirl. I must say in my own defense, that I have only played Half-Life 2 : Episode 1 once. I was just provoked into over thinking the whole thing from Alyx’s contrasting reactions to the abused pawns of the Combine.

Death is interesting. I think the Christian concept of the “second death” is also interesting, that you can die, be raised from the dead at the end times, and then die again.