I believe in the Nautilus case that it was decided upon that "Icons on the desktop" is a major feature for many people. And since Nautilus is the application that does this, it was embedded to default.
The idea to merge the device management into Nautilus was an interesting choice, but when Nautilus was the primary gio/g-vfs management tool, I guess it made sense from an ease of implementation point of view.
Note that this was also set to change again for 3.0, where it was decided that the desktop was no longer to be used much as such with gnome-shell, so it's likely that the device management be branched out into it's own daemon(again?).
But frankly, I see no good reason to make a shitstorm that you find "icons on the desktop" to be such a misfeature that you have to, gasp. Configure it to off.
(Don't forget to toggle off the "exit with last window" check too, for device management when you don't use Nautilus in desktop mode)
Also, if you look at the session settings, you can disable the panel completely via another one of those oh so horrid gconf settings. I'm sure you'll be pleased to hear. And since window decorations are such a nuisance for a purist lightist like yourself, why not disable the windowmanager as well while you're at it.
Frankly, in a metriocratic development, like any desktop system that actually aims for mass appeal, deciding that you do not want an integrated part of the "Desktop" metaphor is an outlier.