Growing up I was in a similar situation. My "biodad" left us when I was less than a year old. From that time until I was about 12 I had to see him everyother weekend, half of my school vacations, and half of the summer. I hated it! He was never home to spend time with me, he always thought it was fine because I'd be over there spending time with my sisters. Well when I was 12 he told me I could start to decide when I would go visit him. Well, I never went... he called me a year later to inform me that he had already moved across the country. (Thanks dad...) I saw him for a week when I was 16 and I had realized that we had NO relationship what so ever. About 6 months before I turned 18, I spoke to my mom about having my step dad legally adopt me. (He married my mom when I was 6, he IS and has ALWAYS been my dad.) So we took the legal steps for the adoption and name change. Unlike your ex, my biodad wasn't going to have it. They tired to come up with every reason in the book why I shouldn't do it. (I'm too young, my parent's were brainwashing me, I need to be out on my own for a while to make my own decisions, etc.) But the judge didn't care. He saw that my relationship with my step dad was the type of relationship a father/daughter should have. So he approved it.
I think that if your daughter feels closer to her step dad, let her do it. Honestly, it really didn't change my life that much. But in a way it was my way of thanking my stepdad for all that he has done for me. It has been about 8 years since I made the decision, and I don't regret it at all.
SORRY that this ended up so long, I hope it helps.