At some point the Inquisition should/will be dismantled, but not in the immediate future. It's not a point that was as loud as YOU ARE TRAVELING WITH A WOLF GOD, but several people talk about organizations falling to the corrupting influence of power over time, despite the intents of a few people to keep it moral. The Seekers. The Chantry. The Elvhen Gods(or equivalent elf government). These are organizations that started out with a purpose, or with a definite moral compass, and slowly became more convoluted and corrupt over a long period of time.
The original Inquisition, on the other hand, changed its purpose and layed down its arms when the original one was filled. Mother Giselle states that many of the people involved became the Templar Order (which also got corrupted, partially due to drugs though). The main point of her story was that powerful organizations can do great things, but their leaders must also recognize when it is either no longer needed, or not the correct force of influence needed in the world.
The original purpose of the new Inquisition was to restore order, and bring an end to Corypheus. We can check both of those boxes at the end of the game events. Rifts may still need closing, but the Inquisition as a whole doesn't need to be in full force in order to commit to reconstruction. Therefore, the Inquisitor (or its advisors) need to find something for it to be dedicated to, or need to start slowly and responsibly deconstructing its power.
Obviously this won't happen over a matter of weeks, but the choice is still there. Retain the Inquisition and find new purposes for it over the span of the Inquisitor's lifetime, or dial back after plans for reconstruction are under way. Future DLC will give our Inquisitor's a new immediate target, or paint the way to the mysterious people lingering in the shadows waiting to strike, if the epilogue is to be believed.