This is a super huge question and unfortunately I'm currently away on fieldwork and so can't write too much, but I see in 4 days no one has responded, so I will at least give you a partial answer. Normally your question would be right up my alley, but I'm far from both my library and a reliable internet connection. Apologies in advance.

It hints at the civil war being as much a revolution of the Han over the Manchu.

This is what I believe to be the most accurate reading of the period. AitHK does a good job at framing the Taiping Rebellion. I think the characterisation of it as a civil war is spot on. This actually gets into the Hakka stuff below, which I'll overwhelm you with links about, but the short answer is "not very" and the longer answer is "it depends on where". In the far South you saw not segregation, but tensions which had developed between groups precisely as a result of living in close proximity.

I've written a good amount about the Hakka, some of which will also address this. I'd actually recommend just taking a look at the following for the Hakka-related questions:

• Who are the Hakka?
• When did the Hakka identity form?
• Should there be more attention given role did the Hakka people played in Chinese history?
• On the Hakka-Punti Clan Wars (part of another question)
• How did the Hakka people come to be acknowledged as Han Chinese?
• More on the notion of Hakka as Han

As to the question of the Qing government and just how Manchu it was, this I can't offer anything in-depth about. However I would recommend asking (posting) again in hopes that one of our other China specialists might notice.