The answer is yes, I planned it from the beginning. And I didn't.
It's difficult for me, even as the author, to trace back when and where the various threads of a story began. I wrote all three of these books in a row, and to me, they're one long story. Yes, I chose three distinct segments of time over the five-year span, and separated out those chunks. But it's all part of a whole, which is why it was so important for me to be able to write this series as one singular book.
So, if I go back to my very first notes, will it include a discussion of Sazed becoming God and using the stories in his metalminds as guidelines for remaking the world? No, I don't think it's there. Just like Kelsier wasn't originally planning to create a rebellion through his sacrifice, just like Vin wasn't even originally female.
Things change and grow with a book as you write it. However, let me say that I knew early in the series that I wanted Sazed to end up as the Hero of Ages and ascend with the power. I felt it was the only way to deal with the world ending and have it start anew. Plus, he's the only one who really deserved it, as he was the only one of the characters who ever cared much about religion.
I kept this in mind while revising the first book, as I'd finished the rough draft of book three by that time. I planned how to use his religions and feature them in the novels in a way that would show off their finer qualities.
In a way, this is my compromise. As I've said, I don't believe in the "spokes on the wheel" theory. Not every religion can be true, if only because they—logically—disagree on so many points. But every one of them can teach things that are true. This is something I actually believe. And, like many of my beliefs, it ended up influencing how I wrote this book.