If it were me I would go ahead and remove all the .gnome related directories, especially since this seems to involve just one user. When Gnome starts up it will create any default directories or files that it needs. For example, when you create a new user their initial home directory contains very little until Gnome or other programs run creating hidden directories and any files that they need to store info between sessions.
I don't have a lot of experience with KDE, but highly doubt it is dependent on .gnome* directories. If you don't feel safe removing these files and directories move them to a subdirectory or back them up somewhere.
Last edited by wmakowski; 09-26-2005 at 10:54 AM.