I'm not familiar with AFCAD editing in FS9 as I am an FSX user, but there probably is an ADE equivalent for FS9 (a free AFCAD editor). If so, I would probably just delete the jetways and if you wanted to, you could delete the entire building.
I am mostly waiting for FSDT's update for JFK but seeing that that may not be for FS9, you could try what I suggested above.