I know that feeling. When I was 14/15 people (also what I believed very close friends of mine) would just say how I was "of a different kind of beauty" and I would just get pissed off cause I wasn't really begging anyone to tell me I am beautiful, since I have always known that I am quite ugly. This is even worst when your therapist is the one who tells you that.
I would tell you not to think too much about it. I've changed 8 therapists and the only thing they made me understood is that you can't take their words for gold
(Funny thing: My third one had the great idea of telling me -sexually abused by my baby sitter for 7 years) , instead, that I should show more my beautiful female features...and he said that in a way...with a look that I saw in his eyes (maybe it didn't really existed, who knows) that I just proceeded throwing up on his shoes.)

Therapists are people. People make mistakes. People can't even express themselves properly sometimes. People are just too arrogant and mean some others.

Maybe there is a point in what your therapist was saying, but she didn't express it properly.
I read about a study on the characteristics that attract people the most. These are pretty general, and work more with a subconscious way that it's used, for istance, sometimes with certain types of advertisment or commercials.
For example, like shezbut's case, eyes a bit apart are more attractive than very close eyes, or a oval face is generically more attractive than a round one.
But these are extremely standardized beauty canons. Some people are more suscetible to them than others. This doesn't mean that a person with a round face is not attractive.(examples? Catherine Zeta-Jones, Michelle Williams...)
Your therapist offered though a good idea(that people don't look all the same, thank god!),but she developed in a horrible, awkward, and eventually rude way, making you feel like a kind of alien. You should have laughed at her cause she probably didn't know what she was doing and what she said was soooo immature and not worth considering. I don't know what you look like. But what I know is that there are not real butterfaced people =)
Being a woman and not a girl anymore if you don't have a standardized face it will only come for good, since it's surely gonna be more interesting. But whatever is the face you have or the body you have, whenever you feel ugly, just raise your head and feel beautiful. As my granma says "show you are a 100 even if you are a 50, cause what you show it's what people are gonna see".
You have a nice personality? That's so much better of being just a canonic pretty face. Because if your nose is like all the Connecticut but you are proud of that and show yourself strong, you will look a lot more stunning than someone who has a perfect french nose and is completely empty and boring.

A friend of mine works in the fashion business and we often talk about beauty and stuff like that, so mine is not silly bulshit said to make you happy, don't worry =) (also, I don't know you, so I could have just ignored this thread if all I had to say was a bunch of lies =) )

I hope that slightly helped making yourself sure you should have just said to that woman that if she has some freakin inferiority complex she better keeps that out of her work, or it won't be a surprise if nobody will look for her help any further