hi! first of all, thanks for your comment - I'm glad you're enjoying the game, and I hope you continue to do so<3
To address your questions:
1) the civilians don't know you - they don't have any clue about the extent of Scytha's experimentation, and they don't know Rohan. particularly at first, they have no reason to believe either you or Rohan about what's going on, and when (if) the MC explains, they don't automatically start trusting you. Ki-Ha in particular distrusts you as Scytha staff, and Leanna, frankly, is more concerned with keeping her family safe than your feelings. she has no guarantee that any attempt at revenge on Rohan isn't going to have collateral damage, after all.
2) Joia also doesn't know you - she's a kid, and she's frightened and among strangers, and yeah she leans towards you as the person who saved her, but she leans towards Rohan as a person who is nice to her, and any show of violence from any of you is frightening to her. again, she has no reason to trust you except for your behaviour, which can be aggressive and erratic, and the reasons for that aren't clear to her.
3) Rohan is projecting a lot onto you - this is a deliberate character choice. Xe is a dick, I'm not denying that, but xe has reasons and xe's behaving that way deliberately. it's a defense mechanism, and it'll be explained in later chapters, but if you're not interested in that development, there is a very easy way to not have to deal with it beyond chapter 3 :)
4) if you're talking about on the station in chapter 3, xe doesn't bring IVI with xem then - she's left on the ship with Ki-Ha and Rhaxa. if you mean on Portia's ship, it's because the operative is very conscious that their rescue hinges on them behaving themself, and again, portia doesn't have the context to know if any sort of violence is 'justified'.
the operative isn't a person who inspires great trust in people - you show up on Leanna's ship, waving a weapon around and carrying a child who clearly isn't yours, you can potentially make threats against multiple other people in that first five minutes, and your behaviour going forwards doesn't exactly suggest //safety//. Nash also has their reasons for maybe not reacting as intensely as you might expect, which will come out in later chapters, but I have to say, I also think like... Leanna's reaction boils down to her asking you not to be violent around her family; Ki-Ha is pretty understanding, even if you did choose certain options in chapter 3, and Nash will offer to kill xem for you. I don't know what kind of a response you're hoping for, but they all have their reasons for not encouraging the operative to go on a violent rampage while they're trapped on a ship with you.
I hope this cleared some things up for you! thanks again for the comment<3