Admiral Cain* was a great character. She was everything that Starbuck wanted to be: tough, respected, had her shit together, got what she wanted, stuck with her convictions, and didn't sleep with Baltar. She wasn't without her flaws, obviously, seeing as she had Roslin and Adama planning her assassination, but as I've stated before, it's not like she was this amoral creature who made decisions based solely around her ego (hi, Baltar!). She just simply lived in an echo chamber, unlike Adama, who had Roslin and his own son acting as his conscience. I can't say that I'd have made the same choices that she did, since she is definitely more of a T (thinking) on the Myers-Briggs test than I am**, but I can at least understand the methodology behind them.
Cain's treatment of Gina was abhorrent, yes, and in spite of my fondness for Cain, I did feel a bit of justification when Gina shot her in what I assume was her head. But if I were to be completely honest, I partially wish that Baltar had killed Gina out of mercy when the resurrection ship was destroyed. Sure, she wouldn't have gotten her revenge, but he basically had to convince her that, nope, what she really wanted was to go and kill Cain, although there was no guarantee that she'd be able to get into Cain's quarters without being seen by one of the many members of the military most likely on regular patrols. Hell, she might have just been shot on her way there, since everybody knew that she was a Cylon***. But here's the thing: Baltar's supposed support of Gina was exceptionally selfish. He wanted a relationship with her; he was disillusioned with his Head-Six and his Head-Apartment overlooking the lake. He completely disregarded her emotional pain of being raped, multiple times, and tortured, hoping that she'd just, oh, get over it and he'd be able to have his Six back in real life, instead of some messenger from God that had begun to irritate him. God, Baltar, you are such a dick.
This way, Admiral Cain would not have been executed, and the writers could have explored so many interesting stories with her. She had already shown that she could back away from making pragmatic, yet immoral actions when she rescinded her orders to kill Adama. A partnership/rivalry between her and Adama could have organically developed, and she and Roslin could have learned to respect each other as strong leaders, even if they didn't always agree on things. Had Cain not been killed because of fucking Baltar's meddling, she might have been able to handle Fisk's involvement with the black market, which occurred oddly quickly, considering they'd only been with the fleet a few weeks and he'd been in command of the Pegasus for an even shorter period of time. Seeing that Cain viewed the military as a priority, she wouldn't have stood for his behavior and would have demoted his ass for even lowering himself to that level. And for another check mark on the plus column, Lee wouldn't have been handed a battlestar, and maybe he would have phased into a life of politics way before he did. She could have also developed her mentor-like friendship with Starbuck, who really could have used a "strong female" presence in her life to inspire some sort of discipline, and I think that would have played off really well with Starbuck's familial relationship with the Adamas. While it is possible that the Cylon sympathizers would not have formed a cohesive unit, I do think that they would have been informed that Caprica-Eight was helping the fleet. This alone might inspire them to create the group, although not with the radical, violent protest model that Gina gave them. But for plot's sake, let's say that some of them do choose to go the blow-shit-up route and the Cylons come to New Caprica after a nuclear device is detonated. This still presents the opportunity for Admiral Cain to redeem herself for her earlier actions; she originally leaves with Commander Adama, as Dumbass Lee does at the end of the second season, but after spending several months away with the commander and bonding with him over the rescue efforts for the New Capricans, she - again, like Lee - chooses to use her ship as a battering ram, instead opting to go down with the ship that helped her survive for so long for the greater good of the fleet. Then the torch could be passed on directly from her to Adama via the comm to lead the entire human population to Earth.
Going back to the Cylon sympathizers, I'm not even sure, had Gina been given her wish for Baltar to kill her, they would have formed a cohesive unit, but to be honest, just because the Cylons were able to trace a "signature" from the warhead that destroyed Cloud Nine doesn't mean that they wouldn't have found the humans, anyway. Caprica-Six and Boomer obviously didn't have the effect of truly changing the minds of the Cylons on the whole, and the toasters seem to have an uncanny ability to find humanity (they are their children, after all, and the best way to ensure that a kid is going to find something he wants? hide it where you think he can't do so) without the aid of nuclear blasts. The story could have continued as it did, but instead of just one year following the settlement, since it probably would have taken the Cylons a bit more time, we could have fast forwarded possibly two or three years. I mean, I know a lot can happen in a year, but I find it really difficult to believe that Starbuck and Tigh would have been as buddy-buddy as they were after only twelve months on New Caprica, since a big portion of their previous interactions were about how much they despised each other, professionally and personally.
Gina wasn't necessarily a likable character - she was responsible for assisting in the genocide of humanity, claiming to be a soldier completing her mission - but she was sympathetic, considering her brutal treatment at the hands of the Pegasus crew. Like I said above, had Baltar shown any kind of empathy for her, he could have ended her torment and, believe it or not, provided a sense of stability after the destruction of the resurrection ship. True, this is just my writer's intuition here speaking, since this is the direction I would have taken the show. Despite Adama's disagreements with Admiral Cain, he had a great deal of respect for the woman**** and would have happily given up some amounts of authority and responsibility to her, once she proved that she wasn't just going to strip the civilian fleet for parts and personnel. Given the theme of Baltar's later trial for treason, Cain would have probably been one of those who voted to acquit the man, based on her own choices that should have been grounds for her own execution. But nope, we had to let Gina live and get her revenge on her once-lover. Oh, well.
* Not gonna lie, Michelle Forbes is one of my favorite actresses ever. I've loved her ever since she showed up in Star Trek: TNG as Ensign Ro Laren. When I found out that she was going to be in Battlestar Galactica, I got ridiculously excited, kind of like I did when discovered that she's going to be in The Hungers Games: Mockingjay Part 2.
** It's actually kind of scary how far F (feeling) I am. The other typologies tend to be more even: I'm almost 50/50 on E (extroversion) and I (introversion), 60/40 on S (sensing) and N (intuition), and 70/30 on P (perceiving) and J (judging). But with F? Yeah, the T is nearly non-existent.
*** I still find it somewhat unbelievable that Gina was able to navigate the Pegasus without being detained at least once or suffering some sort of injury that would have prevented her from getting to Cain's quarters. Which brings me to another point: did she have a key - the thing that Cain has to use to get into her own fucking room - tucked somewhere in her new uniform? Did Baltar provide it for her? If so, how did he get it? Or did she remove the plating, figure out a way to open the door and then magically replace the scanner so Cain would be unaware that anyone had tampered with the door? Maybe she used ventilation shafts? This makes no sense to me, actually. Oh, well. FANTASY.
**** EJ Olmos continued his Castillo trait of only looking people in the eye if he respects them, and even while he's royally pissed at Cain for doing what she does, he still holds a steady gaze with her.