Comments about full of scruples about her scruples, please!
To lay hands on the Hatchard ark
was a grave matter, and Miss Hatchard, always full of scruples about her
scruples (it was Harney's phrase), wished to have Mr. Miles's opinion
I think it means just what it says - EW is developing two characters at once - Harney and Miss Hatchard. Miss H not only has scruples (about what is right) but also scruples about those scruples (whether it's right to have those scruples).