Actually, turns out there's a much easier way. Can you try this patch? 
I see the Thunderbolt controller after resume, although it doesn't seem 
to be in a working state.

commit 102547d63e2cbbda42a25f650df9a33cf929a385
Author: Matthew Garrett <[email protected]>
Date:   Mon Mar 3 18:49:28 2014 -0500

    ACPI: Support _OSI("Darwin") correctly
    
    Apple hardware queries _OSI("Darwin") in order to determine whether the
    system is running OS X, and changes firmware behaviour based on the answer.
    The most obvious difference in behaviour is that Thunderbolt hardware is
    forcibly powered down unless the system is running OS X. The obvious 
solution
    would be to simply add Darwin to the list of supported _OSI strings, but 
this
    causes problems.
    
    Recent Apple hardware includes two separate methods for checking _OSI
    strings. The first will check whether Darwin is supported, and if so will
    exit. The second will check whether Darwin is supported, but will then
    continue to check for further operating systems. If a further operating
    system is found then later firmware code will assume that the OS is not OS 
X.
    This results in the unfortunate situation where the Thunderbolt controller 
is
    available at boot time but remains powered down after suspend.
    
    The easiest way to handle this is to special-case it in the Linux-specific
    OSI handling code. If we see Darwin, we should answer true and then disable
    all other _OSI vendor strings.
    
    Signed-off-by: Matthew Garrett <[email protected]>

diff --git a/drivers/acpi/osl.c b/drivers/acpi/osl.c
index 54a20ff..ef8656c 100644
--- a/drivers/acpi/osl.c
+++ b/drivers/acpi/osl.c
@@ -156,6 +156,16 @@ static u32 acpi_osi_handler(acpi_string interface, u32 
supported)
                        osi_linux.dmi ? " via DMI" : "");
        }
 
+       if (!strcmp("Darwin", interface)) {
+               /*
+                * Apple firmware will behave poorly if it receives positive
+                * answers to "Darwin" and any other OS. Respond positively
+                * to Darwin and then disable all other vendor strings.
+                */
+               acpi_update_interfaces(ACPI_DISABLE_ALL_VENDOR_STRINGS);
+               supported = ACPI_UINT32_MAX;
+       }
+
        return supported;
 }
 

-- 
Matthew Garrett | [email protected]
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