You guys are probably all aware of this, but it seems like one solution is to
have the bootloader kill the NV96 card on boot, if you're using grub2:

https://help.ubuntu.com/community/UEFIBooting#Selecting_the_graphic_card
http://askubuntu.com/questions/149921/how-to-add-a-command-permanently-to-grub2

One could also make an early quirk that does this as well based on a DMI match.
I wrote up a quick patch to do that, but it's completely untested (see below).
I doubt it'd be upstream-appropriate though, as it would kill the possibility
of using the second card entirely.

diff --git a/arch/x86/kernel/acpi/boot.c b/arch/x86/kernel/acpi/boot.c
index 230c8ea..8cb7665 100644
--- a/arch/x86/kernel/acpi/boot.c
+++ b/arch/x86/kernel/acpi/boot.c
@@ -1357,6 +1357,12 @@ static int __init dmi_ignore_irq0_timer_override(const
struct dmi_system_id *d)
        return 0;
 }

+static int __init disable_macbook_second_video(const struct dmi_system_id *d)
+{
+       outb(0, 0x750);
+       return 0;
+}
+
 /*
  * If your system is blacklisted here, but you find that acpi=force
  * works for you, please contact linux-acpi@vger.kernel.org
@@ -1432,6 +1438,15 @@ static struct dmi_system_id __initdata acpi_dmi_table[]
= {
                     DMI_MATCH(DMI_PRODUCT_NAME, "TravelMate 360"),
                     },
         },
+       {
+        .callback = disable_macbook_second_video,
+        .ident = "Apple MacBook5",
+        .matches = {
+                    DMI_MATCH(DMI_SYS_VENDOR, "Apple Inc."),
+                    DMI_MATCH(DMI_PRODUCT_NAME, "MacBook5"),
+                    },
+        },
+
        {}
 };