Look on the USGBC website for the multiple buildnigs and campuses application guide. This is only applicable to LEED-NC v2.2, and has not yet been updated for LEED 2009, but it may help you understand the situation. Since USGBC has not offered definitive guidance for LEED 2009 projects, I would recommend that you check with GBCI.
My understanding from reading the Minimum Program Requirements is that you CAN certify a building with less than 1 FTE. The only hitch is that you cannot earn any IEQ credits, and you must meet the IEQ prerequisites.