I don't see how following the user interface guidelines makes MC less of a native OS X application - MC uses it's own system to draw the windows, regardless of platform. With your logic, the Windows build wouldn't be considered a native Windows application or native the Linux build wouldn't be considered a native Linux application, but they are. MC isn't the only application that doesn't follow the Mac's user interface guidelines, Steam is another example. I wouldn't be surprised if Adobe's applications on OS X are the same in this regard as well.
This issue has little to nothing to do with the user interface (or the debate of it being a "native OS X app or not"). I believe the issue lies in the smooth scrolling effect used within MC - if this was removed/changed, I'm sure the scrolling performance in the Mac build would be much, much better. I can already open the Mac's System Preferences > Mouse and increase scrolling speed by one or two steps, which in turn improves the scrolling speed in MC. This isn't the ideal workaround or solution, but it does work to some degree (and honestly with default scroll speed settings the Mac seems a bit 'slow' when scrolling, IMO).