First, lets clear the confusion between been and being.
As a general rule, the word been will follow any form of have (i.e. has, had, will have). On the other hand, being is not used after have or its forms. The word being is used after to be and its forms such as is, was, were.
She had been treated with these medicines in 2004 - means In the year of 2004, she was treated with those medicines. Using had been instead of was here would give a little connection to the present time (when this is spoken/written). One more thing, had been is a complete process. The thing has happened fully (I was in New York and I had been to New York -you completed the procedure of going and coming back). About this topic, read here.
She had being treated with these medicines in 2004 - does not sound grammatical. Something being means one's self and is not used in such context.
You say Being a tall person it's difficult for me to fit in a small car. Check that - being is referring to self. In this sense, if you want to tell that someone was treated, somebody's (self) was treated, you use being but then, it would take is/was as I wrote in the beginning. She was being treated....
Now the second example -
She said as she had earlier been treated by the Guptas, in May 2003.
The sentence is in passive and thus, I'd recommend using that.
She said that she had earlier been treated by the Guptas, in May 2003.
Good read here and here.