This counter-analysis is too long already, so I'll leave on one point:
That the show as a whole shows religion, particularly Christianity, as being a good thing, it has shown bad qualities about the Christian religion, like how Christian preachers do need do pull stunts to get the church funded and put asses in pews, but on the whole the message is that religion in general, and Christianity in particular, are good and valuable things for people to have in their lives. In the end the diagnosis is that it is good.
For example, Homer stops going to church, while some parts of this show him as making points about how "God is everywhere", and that "he should be able to worship God in his own way", this is shown as him being lazy and entitled.
At the end of the episode, he realizes that religion is important, his life is saved from a burning building by people of various religions, including Krusty (a religious jew) and Apu (a practicing hindu),also Flander's house gets set on fire, but god immediately puts it out, and Flanders is supposed to be the morally straight ultra-Christian stereotype, homer then goes back to attending church after this.
Matt Groening is himself a Christian, he's a liberal democrat, but a Christian one, at least that was last time I saw him talk about his religious values in an interview, which admittedly was a while ago, but those were the days when he was making episodes like these.
Since then his spokesperson in the series, Lisa, converted to Buddhism, so I'm guessing he was following the trend of Eastern religion among liberal celebrities back then.
It's shown that Christianity has saved lives, it's gotten people through tough times, helped people in need, given people a sense of purpose and moral guidance, given people answers to tough questions, and it's created a community that has been of great benefit for those who belong to it.
The Simpsons position on Christianity is like it's position on liberalism, it can at times show the worse parts of it, but for the most part, it treats the ideas associated with the political ideology far more positively than any alternatives, of which the show features just one, republican conservatism, which is depicted as being a wholly evil ideology of millionaires sitting around a table talking about how best to fleece the poor.
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