I agree, and I actually had the opportunity to discuss that issue with members of the Joomla! core development team while attending the OSCMS Summit a couple of weeks ago.
They seemed to agree with me, and indicated that the issue would be handled differently in the upcoming 1.5 release (which is already in beta). It was interesting to learn that one of the main reasons they left the recommendation to leave magic_quotes GPC on, was to facilitate the most popular Joomla! add-on forum, whose conversion scripts to move data from existing phpbb and other forums data into the new forum relied upon it.
Additionally, it is possible to suppress the warnings in the back-end via a setting in the Joomla! back-end, and that is probably a good thing to do if developing a site for others - that warning might make your client feel as though they had an “exposed” system, which really is not the case.