Is it rude to refer to a woman as "she" in her presence?
Yes, but it kinda depends on what you're saying. If you are referring to someone who is present in the third present, regardless of the gender, is rude or at least is something you must avoid.
If you use pronouns such as he and she during the conversation which that person is present in, it makes them feel that the conversation is about them, not with them. It really makes an uncomfortable situation for him/her.
When you are having conversation in a group, you should call them with their name or use you if you need to instead of using he/she.
Sometimes, it also depends on what being said. For example, if you introduce your friend like:
This is John. He lives in Manchester.
It is not rude. However, if you say,
He will now do this.
This might be rude, because you're not asking that person directly.
In case of given example in the question, there is a little chance or it is very unlikely that she will consider it rude.