The Defiant pathfinder presumably isn't canonical (or did it show up on an Okudagram?), and neither is Rick Sternbach's origin story of the Nova-class, which says that an admiral reused the pathfinder concept once it had been abandoned. However, if you want to work it in, we can always suppose that the Defiant parts on the pathfinder were smaller than on the DS9TM top view, or maybe they were scaled down for the Defiant, BoP-style, though I don't like that idea. Either way, this would be a weak argument for resizing the ship.
(Offscreen, the pathfinder was obviously designed with a 171m Defiant in mind, since that is the figure used everywhere in the book except in Doug Drexler's MSD and deck plans -- yes, even in Doug Drexler's exterior views, which is why I don't believe he ever measured the length of his interior drawings.)