Rem's actions aren't totally justifiable. Emilia says as much in the WN:

[Ram: Barusu was already under the curse’s effects by then]

[Rem: Yes, it is as big-sister-sama said. Subaru-kun was weakened to the verge of death. The curse’s effects had sapped his life-force to its absolute limit, and I determined that saving him was impossible……]

[Emilia: And so you crushed him to death with your flail. ――That only added to his suffering]

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It was a convenient excuse to murder someone she didn't like because he smelled like a witch cultist.