Being timid is normal, the fact is many girls have been hurt before and are often leery of new people.....even more so ones that are married. If you are not divorced yet this is a major concern for her. The best thing to do is to continue to let her know you are not living as a married couple and have in fact been separated for five years.
It sounds like she is shy to begin with, so this is going to take a little bit of time. Since you are shy as well it will help if you can try to be more confidant and let her know that you are willing to take this at her pace. If she thinks you are pushing then she may pull away. Let her know you really like her, and do not want to scare her off so you are willing to go at her pace.
Maybe talk to her friend and see if she would like to do a double date (This is where you go out with the girl, and her friend comes along with her date) this will help her by seeing that you only want to go at her pace. Often women feel better in groups, so by doing a double date she may feel more comfortable.
Also try smaller dates, like a lunch date or maybe going somewhere on a Saturday afternoon. This is less intimidating to a women and gives you a opportunity to get to know her without all the pressure of a evening date.
Take things slow, and you will find that it will work out better.
It does sound like you are worrying over nothing at this point. She is going to want to move slow because of everything but you have shown her that you are willing to stand up for her and do the right thing so that is a big plus on your side.
I would as her friend about coming out as well..........this shows her that you are not just interested in getting her out and becoming intimate with her. Many women become a little afraid thinking that the guy may talk her into sex on the first date so make sure you are not pushy in that regard. A friendly kiss good night and this will help her see that you are interested in her and want to take it at her pace.