Isotopes in the recently excavated bones of a 14-year-old girl from th

This is what the sentence tells us:

Isotopes in the bones indicate:
1. She ate a high protein diet when she was alive
2. She was the daughter of a gentleman; she was not a maidservant.

The use of "maidservant" is a hint that we are talking about her, not her parents. Else, we might have said "she was not the daughter of a servant". In those times, the father's occupation used to decide the children's fortune. In any case, you don't have to know this. The available options clarify what is meant.

(A) that she had eaten a high-protein diet, so was probably the daughter of a gentleman, not a maidservant

(B) that she ate a high protein diet, so probably had been the daughter of a gentleman, and not a maidservant

(C) that she had eaten a high protein diet, so was probably the daughter of a gentleman, and not a maidservant’s

(D) she ate a high-protein diet, so was probably the daughter of a gentleman, and had not been a maidservant

(E) she had eaten a high-protein diet, thereby had probably been the daughter of a gentleman, not a maidservant’s

The logical structure here would be: She was A, not B
e.g. She was intelligent, not stupid.

This does not make a lot of sense here: She was A, and not B.
e.g. She was intelligent, and not stupid. - Incorrect
'and' implies two qualities. But we are talking about one quality only - intelligence. 'Not stupid' implies 'intelligent'.

It would be alright to say: She was intelligent and not lazy.
Here we are talking about two of her qualities: intelligent & not lazy (which implies hard working to whatever extent)

So we should write: ... she was the daughter of a gentleman, not a maidservant

Also, use of past perfect in "she had eaten a high-protein diet" is fine. There is a point in time in the past when the action stopped (when she died).
But use of past perfect in "she had been the daughter of a gentleman" is not correct. She was the daughter of a gentleman and will always be. That state does not change. Just like we say "A invented B". We do not say "A had invented B" because the state is still the same.

If she were alive today, we would say: She is the daughter of a gentleman.
Since she is not alive today, we say: She was the daughter of a gentleman.
It is a state that does not change. There is no point in time in the past that changes this state. So use of past perfect is not correct.

So (B), (C), (D) and (E) all are eliminated.

Only (A) remains in which we are given " ... she was the daughter of a gentleman, not a maidservant"
If the sentence wanted to tell us that she was the daughter of a gentleman, not the daughter of a maidservant, then to be parallel, (A) would have been: "... she was the daughter of a gentleman, not of a maidservant"

"..... she was the daughter of a gentleman, not a maidservant's"
is not good parallelism.

Answer (A)