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examples of stuff that did this is like Fire Emblem 7, Naruto, Fullmetal Alchemist kinda.

I think sometimes though, writers, knowing that the two sides will eventually team up in the end, avoid making certain characters actually kill anyone important. Thereby making it easier for the viewer to accept them when they change sides.

Halo is an example of this, with the Elites changing sides to join the humans. In the levels before that where you play as the Elites, you never actually fight humans. Nor does like the Arbiter ever kill anyone in a cutscene or something.

Kinda cheating, because everyone you kill is a loved one of SOMEBODY, but it's like if the viewer never cared about them then it's easy to just not care.

oh Civil War kinda did this too, although since Bucky was brainwashed I almost don't count it, cuz there really isn't any moral responsibility there

yeah this trope has been a thing, its called Lemon Party after how Finn and Jake have to join forces with Lemongrab after hes killed many citizens of tthe candy kingdom trying to usurp it, and they throw this awkward party to commemorate it.