Try new things and keep track of how well they work. Don't worry about whether your process looks like any other writer's process.
What I don't recommend is beginning at the beginning. Since you need an ending to work toward, begin with that ending.
Endings do need to bring at least the major story threads to a resting point, but they're primarily emotional experiences.
Every single approach to writing is perfectly okay, as long as it's in line with the kind of writer you want to be.
Adding or subtracting a character in the middle of creating a lengthy work is nearly as challenging as breaking up with a longtime life-entangled partner.
Take this significant aspect of your work and see it as a selling point rather than a drawback. Find venues and audiences that appreciate your work for what it is, and keep making the art that you want to make instead of jamming yourself uncomfortably into another mold.
Go ahead, write! You're a writer! Enjoy it! Your book is a mess and that's fine! Many perfectly lovely books start out as messes. Keep on going until you finish your mess.
Being a doormat is not something readers generally find appealing in any character, and particularly in a main character. Give her things to do and let her do them. Let her take risks and sometimes succeed and sometimes fail. Let her pick a goal and commit to it and pursue it. Let her, as you say, make choices. Otherwise she isn't really a character; she's exposition with a face and a name.