((Q4: On the Mystery Train, he (Amuro) said to Miyano Shiho that “My comrades who are tracking us have made arrangements in order to retrieve you”, but were those comrades from PSB? If that’s the case, I’m curious about how he planned to deceive Vermouth…! A: Those were comrades from the Black Organization, so there was no need to deceive them)).
My initial reaction upon reading Aoyama's answer was: "OMG!!! ARE YOU KIDDING ME??!!!" or maybe.. "BLOODY HELL.. WHAT WAS THAT??!!"..WOW.. It's a really big shock, isn't it??
So, at this moment, I really want to thank Gosho for telling us this sadly shocking truth which contributed to change my whole mind on Amuro's character !!
Now, after this brief introduction, let's go ahead into another serious issue that has to be addressed well by Gosho, which is of course.. "Sherry Bourbon.. Face to Face" case that's yet to come. I’m curious to see how Rei and Haibara will react once they eventually meet each other. Moreover, I’m looking forward to the developments that will entail upon this event. But first, Rei has to see Shiho first (who is now little kid), then discover her true identity (and maybe Conan too)
However, until now we know that Rei was planning on handing Shiho back to the BO in the Bell Tree Train arc. But thankfully, that didn’t happen thanks to Conan’s big brain, Kaito Kid who disguised as Sherry, and Akai Shuuichi intervention, which made Rei believe that Shiho died in the luggage cart. Now, he is yet to meet Haibara and discover the truth about her, but when he does, this is how I imagine things will go down:
1- He’ll despise her as a traitor, and because he’ll think of her as a criminal who worked for the BO and developed a deadly drug. However, he won’t be able to hand her back to the BO since he was the one who confirmed her death. Handing her back would only have the BO questioned his credibility and loyalty. Therefore, he’s left with one option; taking her into PSB custody for interrogation. In addition, I don't think Rei will simply believe her if she said “she was forced to work on that drug, and it's not her intention to make a poison in the first place”. So, how can this be prevented ??
A- Conan, Akai Shuuichi, Professor Agasa and even Kudo family can't just stand aside and simply watch, they have to intervene in a way or another to make Rei back off, since they know the real truth about Haibara, while Rei doesn't.. Plus, Conan and Akai promised to protect her, specifically Akai who promised Akemi to do that, and since he knows the real identity of Amuro as "Furuya Rei", he can simply threat him to expose it if he approaches even one inch towards her
B- I feel the tapes Elena recorded to her daughter were more than just the drug’s true purpose. She may have also recorded what the organization forced her and Atsushi to go through. And with the fact that Vermouth seemed to blame Haibara on her parents' research, it is quite possibly Elena mentioned Vermouth on the tapes. If Haibara brings up those tapes and Rei heard them, first of all he’ll get closure (because he loved Elena as his own mother) and finding out about Vermouth’s link to the Miyanos, he can investigate them more. I don’t think it’ll be difficult for him to uncover the truth about her family especially since he knows Vermouth’s secret and that couldn’t have been easy.
C- And for the last point, just like how the Kudo family struck a deal with Rei to work with Akai (I suppose that), they’ll probably do the same thing to protect Haibara, and with time, Rei will learn the truth about her past, and instead of harming or jailing her, he'll protect her.
2- As a second point, considering Bell Tree Train Arc events, not only Rei will despise Haibara, but also, she will despise him especially after discovering that he's in reality a PSB agent, and she will hate him even more after learning his relationship with her mother as he met her in childhood, and loved her as his own mother, and above that, he was willing to use her as a pawn, bringing her back to BO, or worst killing her
Wow, it will be a dramatic scenario if it happens, I have no doubt about it.. I can't wait this drama to happen in DC manga
3- The third point, and it's serious, is the confession of Aoyama in "Let's Talk A Day" in 2019, saying that Amuro and Haibara will get along well

So basically in the end, I’d like to think that once Rei learns the truth about her and her family’s past, he’ll be relieved to have received closure (because he loved Elena so much) and subsequently decides to protect Haibara. Hopefully, he will regret someday for his action with Haibara.. And I can’t wait for him to realise that he was an absolute idiot for willing to sell her out. Hopefully the guilt will hit him like a freaking truck when he knows the truth about everything she and her family went through, and how Haibara's changes and goodness right now
Finally, talking about Amuro's actions, the only thing that comes to mind to justify his attitudes (not that I agree with it) is he has lost his soul after losing all of his friends, maybe his real family, and people he thought of as family (or Elena). He technically has nothing to fight for apart from Japan’s security.
A parallel situation would be Akai and Akemi. He also used her in the beginning; because he was so desperate to find the truth about his father’s death and infiltrate the BO. It was not until Akai fell in love with Akemi that he changed his ways and kept his promise to look out for Haibara.
So I’m just guessing if Rei ever finds that special someone (as cliché as it sounds), he too might change his approach and stop being a self-serving anti-hero.
So, this is only a theory.. maybe right or maybe wrong, so, I have put my effort to explain the situation as I can..and finally, thank you for all your opinions or suggestions