Why so much anguish over the lie? (North and South)

SPOILERS

I was reading chapter 36 last night. Margaret's conscience is tormenting her. She had to lie to a police inspector. Her brother Frederick had risked coming back to England to attend his mother's funeral. This was risky because if caught he would be hanged for a mutiny he was part of while serving in the Royal Navy. The crew had rebelled against a tyrannical captain, and had cast him off in a boat. As bad luck would have it, Fred is spotted my a former shipmate of low character who is working as a railway porter. There is a bit of a scuffle, the porter falls to the ground and Frederick jumps on the train. In another bit of bad luck, the porter has diseased internal organs and he dies a few hours later. (I wondered about that. It reminded me of a case several years ago when a riot policeman pushed a passing pedestrian to the ground. The pedestrian got up, but he was a heavy drinker with liver disease and he died shortly afterwards. Only thing is the porter in the story was relatively young for such advanced liver disease.) Anyway, Margaret was spotted at the scene so a policeman came around to talk to her. Margaret is still extremely worried about her brother's safety, so she denies she was there. In another series of complications, Margaret had also been seen with her brother going to the railway station by Mr Thornton. Mr Thornton was the magistrate who was called to see the porter's dying body when he was brought in. In addition, he is acquainted with the police inspector. He does not know the man with Margaret was her brother, but he knows she has lied to protect him.

This is all pretty unfortunate, but I don't why she is torturing herself so much about the lie. What should she do: increase the risk of her brother being hanged, or tell a lie? She is also very upset that Mr Thornton knows she has lied. Thornton has decided to close the inquest (this sounds legally a bit dubious).I was surprised about all this anguish. I suppose it must have been her Christian upbringing.