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.