Sounds like Gnome and, the 90% really want integration. Makes life easier.
No, GNOME has a very good abstraction of Privs, it is called "only has the privs of the user using the environment"

Which effectively removes the possibility of system exploits, causing heartache for the whole machine. Restore you User $HOMEDIR and you are golden. Of just re-populate with /etc/skel setup and you'll be working in no time.

The Integration is vastly different in comparison of WindowsXP and GNOME.

First of, the integratoin in GNOME does not have the ability to run as another user, unless specifically configured to run different from default. Second, GNOME is seperate from the GUI, which is seperate from the OS, which runs the GUI outside priv'd ring-0. Which then again operates everything as a file. *NIX does exactly what you tell it. *NIX is also tremendously more predictable when the integration actually is working. Documentation, sure there ar a scribbles here and there. But sometimes that is really all you need. I figure it is better to have the facts rather than REEMS of fluff-in-stuff.

Windows, the integration can be exploited to run as a priv'd user without any configuration required. Second the Integration and the GUI both run in the priv'd Ring-0. Windows running things directly in Ring-0 is dangerous. By default you can do things in Windows you should NEVER be able to do period as any user. Windows second guessses you all the time. Therfore Windows is tough to predict with any certainty. Documentation, sure plethora of Docs that were written by people that are paid by the Line. Yeap. Perfect.