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But having to use the app to manage files, is a whole new paradigm that someone has to learn which is exactly what people are trying to avoid in the first place. So either teach one paradigm to a new user and stick to it (aka using the file system) or application specific paradigm (aka use iphoto to manage photos, itunes for music files, etc). So depending on how good you are at controlling the application usage from one app to another you end up having to learn each applications way of doing things instead of learning one way of doing things and using that throughout.

As a developer and previous life as IT support I fully support the teaching the file system paradigm because it works better overall.

All of the tag resorting you are doing within iphoto can and is done rather easily within the file system as well so what has that added other then more complexity?