I think the immaculate conception can be accepted as either the machinations of Darth Plagueis/Darth Sidious (Dark Side), or the Will of the Force itself (Light Side). By removing it as the dubious actions of some microorganism, the interpretation (however you interpret it) has much more resonance with the story.

As for "Queen" Amidala, to me it's pretty simple and clear: Queens are not elected, they're born. Queens can take the throne at the age of 14. It's happened in monarchies before. But no core planet in their right mind would elect a 14-year-old as a ruler. Naboo's tradition of electing kids to the top office is just plain stupid. Thrust the throne on her by happenstance and you have a believable story. And as the Queen matured, she would have increasing clout in the Galactic Senate, as we've seen. Look at Elizabeth II ... she has far more influence now on the world stage than she did fifty years ago.