Thinking it through again I suppose the problem with a capitulation was that, unlike a defeat, it couldn't be denied, minimised or spun into something heroic: there was an embarrassing signed document that could be published in Spain, England and anywhere else in Europe that could brave the censors.
Notably the article which seems to have caused most offence was no 15:
"In several places and notably at the assault of Cordoba several soldiers, in spite of the orders of Messieurs the Generals and the care of Messieurs the officers, carried out excesses which are the inevitable result in towns taken by assault. Messieurs the general officers and other officers will take the necessary measures to discover the sacred vessels which could have been taken and to return them if they exist."
It seems to have been unacceptable even to admit the possibility that French soldiers might have looted churches!
By the way, the phrasing of that clause seems to be the clearest contradiction of the accusation that Dupont allowed Cordoba to be pillaged.
While I think I see better now why Napoleon reacted so badly I still don't see why he pursued the matter as he did; there has to be some history to this - Dupont wasn't a friend of Moreau was he?
regards,
Susan