I just replayed the 1st mission again and noticing the dialogue. Considering we know now that Savathun had her memories erased, probably had her Hive followers remember some about they're relationship-- they were their version of "The Last City". On first meeting, we killed the Hive guardian (probably no worries) but then [b]we killed the Hive ghost[/b]. And Savathun was referring to us as "honored guests" and not as usual 'guardians' but at the same time I think [b]she had sensed some Darkness in us[/b] because of Stasis and so we were strangers to her that came and attacked her people and killed a ghost-- something that "mirrors us" she said. These [b]Lucent Hive were pure Light[/b] already and we were half Light half Dark.
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We have to keep in mind [u][b]Savathun was basically "reset" into a fresh new guardian[/b][/u] and she wasn't who she was before and during season of the lost (much like Crow). Despite how devious Savathun's personality seems, she's still like a good leader supposedly trying to protect her people and the Traveler. I think in their eyes (and even objectively) we were the 'bad guys' in this one.
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The ends don't justify the means. Even if her intentions seem good (to her), they are still incredibly selfish and harming to those she interacts with. For example, even before regaining her memories, she was actively trying to seal the Traveler into her throne world, which would've cut us off completely from the Light and doom us for when the Witness inevitably arrives again.