Question: I work with a group of developers in a company having about 1000 employees. 
A transgender person who identifies herself as a woman has joined our team. 

* She gets upset when we use masculine pronouns (such as "he") to address her, which we obviously do out of habit.
* She also insists on using the ladies toilet, which makes our female coworker uncomfortable.

Taking this to HR is extremely delicate, as they might think we just don't like LGBT people. While we don't want to discriminate against a transgender person, her needs cause issues for us. 

How should we handle this situation?

Answer: 
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First, you should try your best to **address this person with the pronouns they prefer**. I know that this may be hard, especially for people that are not used to working with LGBTX people.

Now, regarding the bathroom, I think that this is something that has to be sorted out with management or HR, as you and your coworkers are not in a position to determine how company members should use the bathroom. 

The ideal thing would be to have a **gender-neutral bathroom**, so this person can use it freely and comfortably. But, in case you don't have one, I feel that this situation *has* to be taken to HR or someone in position of deciding these things. 

No need to *"be perceived as discriminatory"*, as this is a valid concern. This situation has to be phrased something like *"We need to define the use of our bathrooms for any gender identity"* so it is not perceived that way.
I think this should be dealt with lightly. This person is going through a difficult period in her life. I would ignore anything you think of as unreasonable, as any difficulty you have adjusting to her, she is having as well, and moreso because she is getting used to the changes in her body, the changes on how people view her and the changes in interpersonal relationships. Please take all of this into account and show some patience when dealing with her.