A couple of questions still hang out there:
1.) Who provided the prosecution with the knowledge that O'Brien and Hughes overheard potentially incriminating comments from Bates? Thomas would be a likely candidate, but he seemed too wrapped up with trying to get promoted to valet.
2.) Is Cora in any way aware of Lord Grantham's dalliance with Jane? Even if that little sidebar was left unaddressed, I wouldn't mind. It all seemed rather forced and unnecessary.