I have had this question on the backburner for a while and I do wish to come back to it and write a full answer when I can; that said a lot of the scholarship relevant to it I read literally years ago and cannot recall in substantial detail at present and would need to go back over from near- scratch. In general, civilian responses to and reflections on the Taiping War related to the general depredations of the conflict itself and less to the ideological dimensions of the Taiping cause, but Confucian elites did tend towards a stronger ideological critique at the same time. A past Tuesday Trivia post of mine focussing on the case of Zhang Guanglie, who was a child during the war and whose mother was killed during a siege, can be found here

However, while you wait for me to get my act together, I do have a few reading suggestions:

• Tobie Meyer-Fong, What Remains – This is basically the book to read that answers your question most directly; it discusses civilian perspectives on the conflict from a variety of angles. Also see her review of the 2013 translation of Zhang Daye's The World of a Tiny Insect, another memoir of a civilian survivor of the war.

• Indeed, Zhang Daye's The World of a Tiny Insect, translated by Tian Xiaofei, would be a good read in itself, if contextualised alongside Meyer-Fong's book.

• Jin Huan's article 'Stitching Words to Suture Wounds' discusses the diary of Shen Zi during the Taiping War, albeit more as a literary work than as a source on broader civilian perspectives.

• Chuck Wooldridge's City of Virtues includes a chapter on the period of the occupation of Nanjing and elite responses thereof.