To me the red part is not ambiguous, but neither of your interpretations is correct. Of the two, the second interpretation is better. I understand it as:
The last derelict = Lady Frances, is the last member of the direct family who is still alive. She is not rich now, because as a woman she did not inherit; some male cousin inherited, leaving her with little money. The goodly fleet was her father the late Earl of Rufton, his wife, and Lady Frances's many siblings, but they are now all dead.
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