I see the issues involved in answering your questions a little differently. I don't think how Gatsby made his money has anything to do with Daisy's ultimate rejection of him. It may be a bit of a stumbling block, but it's not that much of a problem. I don't think Daisy cares how Gatsby made his money. It's too far removed from her. She cares about maintaining the status quo, and about respectability, to a certain extent. But the issue isn't major.
I give Daisy more credit that some commentators do. I believe the reason she rejects Gatsby is because she does have a sense of ethics. Not in terms of how Gatsby makes his money--again, that's too far removed. She accepts that just as most readers do--look how famous Al Capone is. On the surface, bootlegging is often thought of as a victimless crime. The government was the foolish force behind prohibition, and therefore bootlegging. The government was in error. Haven't we allowed alcohol production and sales ever since?
Daisy's sense of ethics comes into play because, as she herself says, Gatsby asks too much. Gatsby insists that Daisy pronounce that she never ever loved Tom; that she always loved Gatsby. That's how Gatsby loved her. And he insists that Daisy recipricate, that she say that she loved Gatsby the way Gatsby loved her. And Daisy refuses to do that.
She does it at first. Her initial reaction is to agree with Gatsby. She is upset with Tom and knows he's been having an affair. (And please note that this is after Tom accuses Gatsby of bootlegging.) But the second Tom shows a little tenderness, and reminds her of some of the tender moments they've had together, she recants and tells Gatsby that he asks too much, and sides with Tom. She refuses to perjure herself. She did love Tom once, and she refuses to say otherwise.
She refuses to take part in Gatsby's illusion. He idealizes their past relationship and his illusion is dependent upon Daisy loving him as much as he loved her. And that just isn't true.
Think of it this way: Gatsby has as much money, or even more money, than Tom does. Who has the nicer shirts? If money were the issue, Daisy would side with Gatsby. But money isn't the issue. Daisy sides with Tom because Gatsby asks too much.
Finally, does Daisy love her daughter? We don't really know. All we know is that Daisy feels sorry for her daughter, because her daughter is a female born into a male-dominated world. She will face the same crummy situation that Daisy faced: her only chance for social and economic improvement is to be a pretty, little fool, and marry a wealthy man.