I've been having some similar trouble (trying to play Starcraft is tricky with the panel taking up the bottom of the screen!
). I found that setting the panel to autohide, and setting the hidden height to "0" or "1" works well. I looked around and I think that "gconftool-2" is what we're looking for. The keys to change are:
So, your script might look like this:
gconftool-2 --type bool --set /apps/panel/profiles/default/toplevels/bottom_panel/auto_hide "True"
gconftool-2 --type int --set /apps/panel/profiles/default/toplevels/bottom_panel/auto_hide_size "0"
Let me know if that helps!