I did wonder about Cersei's protest at his decision (that part of the book is hazy to me). I wonder if she really meant it, as per Varys' assessment that Ned is more useful to her alive.

yeah I think she totally meant it - she looks away and can't watch the whole thing go down - and I caught her hissing "Stannis!" at Joffrey when she was trying to argue with him. She can't afford Ned dead, because right now the Lannisters are fighting the Baratheon brothers AND the northmen. If Ned had been allowed to live having confessed his treason, Robb wouldn't really have a leg to stand on in terms of "rescuing" his father, the traitor, and Cersei could focus on dealing with Robert's brother.