1) It is not an appositive, which is a noun or a noun phrase.
2) 'Had been" is still required in E because the other event in context is still there (before she was (past tense) ).
3) Should not A be considered more wordy in comparison with E? A and E are both grammatically correct,
I am no expert at this, but I think your point 1 is relevant.
IMO, the modifier between the commas, is not an appositive. But, it SHOULD be an appositive. An appositive, if at all, should have been present immediately following the noun it is intended to modify (George Eliot, in our case).
For instance, George Eliot, a visionary, had been ...
orGeorge Eliot, a popular and respected novelist, had been ...
In both these cases, the modifier (appositive) modifies the adjacent noun, the subject of the sentence.
IMO, in E, the modifier is a clause dependent on the main clause of the sentence. The main clause of the sentence is:George Eliot had been an anonymous...
Because of this dependence, I do not think a construction as in E is possible.
Expert comments are more than welcome. The above is just my interpretation of the question.
Consider KUDOS if you feel the effort's worth it