You can use gconftool with the key /apps/gnome-terminal/profiles/Default/background_type (you might have to use a different profile name than "Default"):
gconftool -s -t string /apps/gnome-terminal/profiles/Default/background_type solid
gconftool -s -t string /apps/gnome-terminal/profiles/Default/background_type transparent
This was tested in version 3.0.1, but the command should be the same.