Of the court - yes, absolutely. Every court case starts with the basic idea that the defendant did nothing wrong. That would be the judge that follows that principle. Is the prosecutor supposed to presume innocence ? No.

It's almost the opposite : the U.S. attorney is not an employee of the justice system, she's an employee of the executive (she represents Obama's interest as head of state - nothing else). She is a lawyer that is in the service of the white house and should therefore defend whatever opinion the executive has on the matter.

In simple terms : if the white house thinks you're guilty the attorney's job is to prove that beyond reasonable doubt. Assuming it goes to trial (which this case did not do) it seems extremely likely that the prosecutor thinks you're guilty, otherwise, why would she start a court case that's likely to publicly humiliate the executive ?

Please keep in mind that the opinion of Carmen Ortiz did not really come into the picture. Once the complaint was filed, and the complainant (MIT and JSTOR) demanded damages, her opinion did not matter in the least - her job is to find a settlement acceptable to all parties involved or bring the case to court (because it's a criminal case). She proposed a number of settlements, which were refused by either Aaron Swartz or MIT, and informed them she would bring the case to court, at which point she informed the defendant of the charges (and included the maximum penalty for them - maximum penalty seems unlikely to have been applied in this case, but that's of course my personal opinion, and I'm not the judge). After that the guy killed himself.

Of course, speaking in general, any attorney would probably like to have good relations with MIT, a place that trains more than a few people who later become judges.