There's the notion that you'll clean everything up in the second draft. I'm writing the second draft of my novel Spirit Quest and I'm finding that it is indeed when you clean everything up, but I never expected to be cutting so much material and rewriting. Perhaps this effect is due to the NaNoWriMO process, which I treated as getting 50,000 words on the page.
I've had a secondary character push herself to the forefront of my story and demand to be cast as a co-protagonist. Rewriting the early part of the story, she fit more naturally into the story and seemed like the perfect character through which to introduce the supernatural. One of my alpha readers also raised this issue as a concern as the main protagonist doesn't really come into play until chapter 3 and is first seen through that secondary character's pov.
I'm not really fighting the process. It's evolving and I'm writing my way out of it. I never expected the second draft to be as volatile as it is. As this story is meant to be the first in a series of novels with these recurring characters, it's actually added more fun to the concept in that it doesn't all have to revolve around one character and each character can shine at different points in the overall story structure.