Interesting post with lots of interesting comments
Sorry for the long reply.
Elli, just to clarify something, a person with both male and female genitals has a condition called intersex, its different to transsexuality which is having the physical body of one gender but knowing that you are in fact the other gender.
For a transsexual its not as simple as accepting yourself and your body and getting on with it. Some transsexuals can do that, for others the pain of being in the wrong body can lead to severe distress and in many cases suicide.
When people are going through gender reassignment and are living as a female then they will prefer it if people use the correct pronouns, she, her, Miss or even simply their name. Same goes for female to male transsexuals with he, him, Sir etc.
Most transsexuals will ignore the odd slip up with pronouns because, if they have decided to go through reassignment while continuing to work at the same place that they have been, they know that people will need time to adjust to things. It tends to be more embarassing for the person that makes the slip up when they realise it. Of course its obvious that you are deliberately using the wrong pronouns, name etc. then it feels really offensive.
What she gets called by her family will depend on the particular family. Some continue to be called Dad, other families come up with another name altogether, some may even agree to them being called some variation of mum.
The toilet issue is a difficult one but there are lots of possible solutions. It also depends on the feelings of the rest of the female staff. If they are happy for her to use the ladies then it shouldn't be an issue. You're not going to want to do anything that any other female would want to do, use the toilet, tidy up hair and make-up and then get back to work. If there are objections then it could be that its agreed that she only uses the toilet when nobody else is in there and that there is a way to let other female staff know when she is in there. Alternatively, if there are toilets that are purely single occupant then it might be that she uses them. Don't forget, if she was to use the male toilets then it would be just as awkward for any men that might be using them.
At the end of the day, nobody wants to make anyone feel uncomfortable. All that's wanted is to go into work, do what your paid for, be treated with respect and dignity, and then go home to your family and friends. Basically to do what everyone else does, each and every day, but with the sense that your body and mind actually fit together properly and aren't completely at odds.
What she is doing is very hard and takes a lot of courage. It can cause immense difficulty with families and friends. Transsexuals can lose family, friends, jobs and homes when they undergo gender reassignment.
Can you imagine what its like to go out each day not knowing whether its going to be a good day and everybody will treat you as a female or whether you are going to suffer verbal abuse, physical abuse or even worse. Its not something that is done lightly.