I don't see how his stance was unacceptable. On principle I agree with him in that someone should not be punished on an accusation. If he had been found guilty of the charges and subsequently had the captain's band taken away from him, then yes.
This isn't the court of law where "innocent until proven guilty" should be elevated as a concept above all others. This is very much an exercise in social re-engineering (to the extent that the aim is to eradicate well-entrenched mores) as it is an exercise in public relations. The FA can't be taken seriously if it is going to criticize Sepp Blatter and create some arbitrarily harsh penalty for Luis Suarez... and yet at the same time not recognize that unlike those other two, Terry has been charged with a crime. The very fact that the Crown Prosecution Service has seen it fit to bring charges means that there is prima facie evidence of criminal conduct on his part.
Terry shouldn't be "punished", but neither should business go on as usual pending the trial. As an example, it is quite commonplace in fact, for employees (both public and private) to be placed either on suspension with pay or some other form of "modified duty" pending the outcome of a trial or investigation. Police officers are routinely assigned to desk duty pending the outcome of investigations into shootings for example, and then just recently the son of the NYC police commissioner, a news anchor with the local FOX affiliate in NYC was accused of rape. He went on a leave of absence pending the outcome of the investigation (it was decided that there was not enough evidence). My point is that there is sufficient precedent for the FA's position that keeping Terry as captain sends the wrong message, given the totality of the circumstances.
All this aside, once the FA acted, Capello should not have come out and publicly disagree with his employer. This is improper under most ordinary circumstances, let alone under the current, given the gravity of the charge. For these two reasons I say his stance was unacceptable.