Two Galactica posts in one week (assuming I find something of any relevance to say about Islanded In A Stream Of Stars come Wednesday) might be a little much, but I’ve been thinking about Boomer a lot lately, and discussing her a bit, too, and I wanted to make a few general points. (Edit: Forget to mention that, once again, here be spoilers).
A lot has been made about how badly Boomer has suffered through the course of the last four years. Just as a brief list, you have being dumped by the Chief, being thrown in the brig (both of which are admittedly entirely understandable), being shot by Cally (less understandable, especially given Cally’s desultory punishment), who later threw Boomer’s kindness back in her surprised robo-face on New Caprica. Next she banned from participating in the “diplomacy” above the Temple of Jupiter, and finally got her robo-ass chucked in the brig again the instant she appeared having rescued Ellen Tigh (of the robo-Tighs).
And that’s just the Colonials. The Threes wanted to box her, and the rest were apparently happy to just ignore her . Their dirty little secret. Either they refused to wipe her mind in case they needed intel on the humans she had once considered friends (and lovers, and confidants, and a family to replace the one she was programmed to mourn every day), or they had offered, been rebuffed (“You carry your scars with a certain pride”) and then just left her to rot.
The Colonial attitude at least is usually put down to their outrage at Boomer’s “betrayal”. Adama can’t look at her without thinking of the scar that lies, quite literally, across his heart. 
I’m sure that’s part of the equation. It might be hard for me to imagine how Boomer can mess with the Admiral’s head to such a degree but the other Eights apparently not register, but then I’m a man who has had precisely zero bullets penetrate his torso (literally speaking, at least), so I don’t hear music and think sirens. If his PTSD wants to explode into being every time he hears a specific call-sign, I say cut the old man some slack.
There’s more to it, though, at least where everyone else is concerned. “You shot the Admiral” just doesn’t really cut it, doesn’t go far enough . Tigh, for example, is the one who makes the call to stop her when she arrives on Galactica above the algae planet. The two machines who deliberately tried to exterminate humanity, and the man who Tigh is convinced assisted them in their second attempt, he lets through. Not Boomer, though. Her crime is far worse.
And it isn’t that she put two in the old man’s chest, either. The problem with Boomer is the problem with Hera: you’re not allowed, under any circumstances, to suggest that the opposing forces in a war lie on a continuum. It has to be us versus them, otherwise everything gets complicated and you have to consider where the boundaries lay, instead of just shooting anyone on the other side of the chasm you’ve conveniently decided exists between you. The Resistance proved that down on New Caprica: suicide bombing is reprehensible unless the people you’re killing are trying to bridge the gap.
The Cylons are on the same page, that’s why they couldn’t consider any way to cross-breed with humanity other than setting up rape farms. If we are to be useful, it must be as a commodity, otherwise someone somewhere will bridge the gap. Caprica and Boomer might have once persuaded them into a cease-fire (and given our only explanation as to what they did came from Cavil who we now now is Captain Evil McLiar, who knows what the specifics were), but that just led to a promotion from tools to badly-trained pets. 
In that sense giving Hera to Boomer to nursemaid was the worst thing that could happen even before the baby rejected her. It was a reminder that the Cylons were desperate to fill the gap, but would never admit to it, leaving her shit out of luck.
And, of course, Hera did reject her. The only proof in the entire universe that humans and Cylons might find common ground, and she didn't want anything to do with Boomer either. Athena, she was cool with. Athena, who hasn't bridged the gap, but somehow crossed it, despite being the one who knew about the holocaust while it was happening, had agreed to help out by fucking an unwitting ECO. I guess a treacherous former enemy gets more points than an unwitting dupe. They've chosen a side, after all, and we'll conveniently forget the fact that Boomer was given both sides, by making sure she could stay with neither.
I'll bet all the money in my pockets that it was very soon after Hera ended back up on Galactica that Boomer signed up for Cavil's Secret Plan To Secretly Manipulate Everyone Club (feat. Secret Ellen). He, at least, understands. He doesn't want to be torn between two worlds either. She might be running from the commitments and loves of her former life, and he may simply want to be the universe's most awesome calculator, but they share the same goal, to reverse the process the Final Five began when they created the first skin-jobs.
To widen the gap.
Someone always wants to widen the gap. That's why propaganda works. That's why Hitler figured out building up Germany would be easier if coincided with tearing down the Jews. That's why Rush Limbaugh has a job, and a radio station, and sufficient money to stuff his face with enough food to satisfy twelve Iraqi refugees, every one of which he would recommend shooting.
Now Boomer wants to widen the gap. Except she doesn't; her parting words to Galen made that clear. What she wants, I'd imagine, is for Cavil to work some more of his memory-altering magic on her. To make her forget she was ever on the other side. That's what made it so easy to fuck Helo, to damage the Galactica so badly as she jumped away. When you've decided to cross a bridge for the last time, you tend to want to burn it, in case you want to change your mind, or in case people try to follow you and bring you back. And because if someone can make you forget the bridge was ever there, then burning doesn't really matter more anyway, right?
Of course, Cavil may be right in thinking Boomer doesn't have anywhere left she wants to go, but that doesn't mean she plans to stay with him. After all. not being able to get back doesn't stop you from torching the side that you're on. If I were a betting man, that's where I would point to as regards Boomer's fate: screwing both sides so badly she can finally feel she has left them, not been removed. It's not a very pleasant idea, and it's certainly not very fair, but it's very BSG.
 Three’s nefarious plan to have both Boomer and Caprica boxed couldn’t have worked had the wider Cylon community been keeping a closer eye on their errant Eight.
 Ishay had to open his chest and massage his heart to get it working again, which I think is medically accurate, but is also a nice little metaphor. What do we do when our hearts are broken?
 Well, I’ll let Galen off as well, since every glimpse of Boomer is a reminder of all the things he’s lost, and all the things he was miserable enough to settle for in their place.
 There's also the fact that plenty of people bitched and moaned that Season 3 was making the Cylons insufficiently scary as their own problems and divisions began to be explored. Even the fucking audience was pissed about the idea of the two sides becoming less distinct. Admittedly, I was slightly pissed too, but that was just because the more time the Cylons spent bickering the less likely any sort of coherent explanation of "the plan" became.