The discrete graphics card can be disabled by using ACPI methods. We're using either bbswitch (a module developed by Lekensteyn) or vga_switcheroo (compiled into the kernel) to do this in Bumblebee.
Since Bumblebee 3.0, this feature is enabled by default, using bbswitch. This allows for automatic PM, without any additional configuration. It's not the perfect solution and may not work on some laptops.