I can understand the desire for options, but in reality I would see the need for the option.
Either I will be playing a 'good' inquisitor who is going to be building the Inquisition with a pretty solid code of conduct, morality, and appreciation for individual freedom into its charter, or I will be playing the 'evil' playthrough in which I probably am going to do it for power and the ability to control and shape the lives of everyone in my domain.
Either character probably wouldn't feel the need to disband the organization they have built, if they believed it fulfills the objects they have envisioned. Now if my 'good' characters end up having to do terrible things with this organization in order to 'save the world' then I would be all for an option to disband it afterward. In the grand scheme of things though, that doesn't leave open many expansion pack opportunities.