Before I get to Gaius Baltar I want to note that in my previous post I had predicted that the young boy, Derrick, that Balter was willing to die for in the episode "He That Believeth in Me" was the 5th Cylon. I thought the lymphocytic encephalitis that killed the Cylons in "A Measure of Salvation" was what the boy had too. Galactica humans are immune to it.
I think I was wrong. The boy is not the 5th Cylon.
I'm betting now that the fact that both the boy and the Cylons had some kind of encephalitis is a red herring to make us wonder if there is a connection. ( Still it's a whole lot of encephalitis going around. Maybe the writers just encephalitis on the brain ;> ) I went over to one of the Galactica forums and found that very idea discussed. Turns out that I heard wrong, the boy was only said to have "viral encephalitis," not "lymphocytic encephalitis" which could be a different virus. I also misunderstood how the term encephalitis is used. Encephalitis is a blanket term for inflammation of the brain. Saying all encephalitis is the same is like saying all cancer is the same. Encephalitis is a symptom, not a cause. Meningitis, rabies, syphilis, and malaria can all cause encephalitis.
I'm not a medical expert and so my initial impression was that it didn't seem possible for a child in advanced stages of such an infection to turn around so rapidly and seem entirely cured in about 30 minutes without some Cylon trickery or a miracle.
I had to look it up, here. And here's what that website said:
"Treatment for encephalitis depends on the virus or other germ that caused it. People with mild cases of encephalitis can recover at home as long as they're watched carefully by a parent or other adult in the household. Most cases of encephalitis just run their course and the person gets better without treatment."
Now it looks like the cult might be fooling themselves, talking themselves into seeing a miracle where it was just nature taking its course. Baltar might be helping them fool themselves, or he might himself be taken in by the illusion of a miracle. He had said the boy "looked worse" when going to the restroom to shave, but that was just a subjective impression by a non-doctor (though in this series Balter also seems to be some super-scientist, a common and unrealistic sci-fi trope that can do anything sciency).
Baltar being a super-scientist just might know he's scamming on the cult's expectations for him.
Let me recap that part of the story to put this in context: First the mother of a young child visited Baltar in prison and asked him to bless her child. The child's mother thinks her boy is suffering a deadly illness (this was never confirmed by a doctor). Then Baltar, while acquitted of the charges against him, is shamed and humiliated in court before all the last remnants of humanity. When Baltar gets out of prison, with more than half the population hating him, that same mother and some of her friends take Baltar to a small monotheistic cult where they consider Baltar to be some kind of prophet or maybe even a "savior." When the mother and sick child are brought to him again, with hopes that Baltar's prayers might heal the child, Baltar says he prayed for the boy, as his mother had asked him to, but we never saw Baltar pray.
Later when the mother questions God, "does God want my child to die," and just seeing the sick child, it seems to lead Baltar to his first moment of honest self-reflection and a sincere prayer. Baltar puts his hand on the boy's head, looks up, and then admits his own humble failings to their monotheistic God, he reveals his feelings of guilt, and then he offers to die in place of the boy. It’s not something he'd have sincerely done in the beginning of the series.
Later yet, as Baltar goes to a restroom with one of the women to shave off his beard, he remarks that the boy seems to have gotten worse. While he is shaving two men come in and one of them tells Baltar how his own son died under Baltar's orders. The two men then make an attempt on Baltar's life. One guy has a knife to Baltar's throat and is starting to cut it when Baltar goes all self-pity and guilt, remembering he offered up his own life, reminded of it by his "Head 6" (the "hallucinated" version of the beautiful female Cylon Baltar knew on Caprica), he tells everyone out loud that he is ready and willing to die in payment for his sins. The guy who was ready to cut Baltar's throat is baffled and startled. He can't kill Baltar so easily now.
Then the woman Baltar came with manages to clobber both men with a pipe claiming she felt God giving her strength. When they go back to the cult's quarters they discover the boy seems miraculously cured.
Now, Baltar had said before that the child's own immune system had a chance of curing the boy, so he might know there is possibly a low probability of a miracle here and also that the cultist want to talk themselves into believing they'd witnessed a miracle. Also the fact that the cult was mostly young, attractive, and sexually willing women could motivate him to want to be seen as their prophet since he does take advantage of it. Or... Baltar might be fooling himself too and talking himself into believing the miracle. That will no doubt be dealt with in a future show.
I don't think Baltar can continually be presented as a lying sack of shit who manipulates everyone, especially not after what he has just been through. If he did he'd no longer be an interesting character, he'd be cartoonishly evil. The writers have done a great job with Baltar's character so far, I don't think they're going to slip up now and turn him into a cartoon. They know that the hook for a villain like Baltar is to make him just sympathetic enough for us to identify our own weaknesses with him, just enough to care. I'm a pretty hard core atheist, but if I'd been through what Baltar had been going through I think I too might pray to a God I thought had a very low probability of actually existing. What harm could it do? What else could he do in that place, he doesn't have a lab or computer? And when you're that low in your own opinion of yourself you just might look anywhere for help, even improbable gods.
Also keep in mind that Baltar's "Head 6" has been repeatedly trying to mindfrak Baltar. She's been trying to push him toward belief in God and the belief that he has been chosen by God. She gives him answers and points him in the right direction. She is always loving but intolerant of Baltar's lack of faith. She is always stern and abusive when he turns from the path laid out by the one true God. This conversion seems to be part of her goal.
It seems to me that Baltar, in his desperation, is now more than sincere enough to consider the possibility of a God. He doesn't have the knowledge of God the cultists think he does, so he's not sincere about that. And as a scientist, and therefore at least a methodological naturalist, he is necessarily going to have real problems integrating such religious concepts as "prayer works" into his world view. (Galactica's writers may not understand the problems though -- at least as those difficulties exist in our world.)
There is something going on with Baltar as far as how he is connected to some source of information through "Head 6" that it seems he shouldn't have. But are the writers really going to introduce a miracle working "one true God" into their story to explain such things? I don't think you'll ever get confirmation on that as a miracle, but it's a wimpy kind of God who's only miracles are sometimes fiddling with life's chance die rolls. Such things are vulnerable to "confirmation bias."
The other thing that seems to be going on with Baltar is that he's discovering that he's having a hard time living with himself. A lot of people died because of his decisions. He's got guilty secrets he can't ever tell anyone about or they really will kill him. He gave Caprica 6 access to the defense mainframe, he knew Boomer was a Cylon and never told anyone. He's done such things, in part, because he hasn't really taken a side in the war and neither side cares much about him. He'd rather have peace, but he has no means to achieve it.
Baltar's guilty secrets only isolate him from the human culture. The Cylons know his guilty secrets and they also know they can't entirely trust him. As someone who, until recently, has been mostly concerned with staying alive I think deep down Baltar would have rather been a Cylon because they don't die so easily. They're the side with the technology and science he adores. As he said before on the Cylon ship - at least he'd have a place that he belonged. He couldn't really fight them before because he wanted to be one of them. He wasn't, when he surrendered, expecting them to be a bunch of Nazis. He's now learned they have some inhuman flaw that he can't live with.
The religious group, in Baltar's eyes, is also flawed by its loony approach to life -- praying and expecting God to do things for you instead of doing them yourself. But it's an easier flaw to learn to live with than is Cylon inhumanity.