Hi, I've tried to make some sense out of the ME documents, and after some study, I've put together a list of the ways mentioned in Intel sheets to disable/stop the ME, and what chipsets they apply to/don't apply to.
I've then included some observations I've made.
If you find this useful (and think it's more likely valid than not), reply, and I'll send a sign-off so it can be put in a patch.

ME disabling methods (all from section 4.5 or section on FPT (Flash Programming Tool):
Manufacturer mode jumper (GPIO 33) (also Flash Descriptor Override)
Works on:
Montevina (Oct 2007 guide) (1), (3)
Intel 3 series chipset (2)
Ibex Peak (4), (7)
Intel 6 series chipset (5), (6)

Remove all memory from Bank 0 (1), (2), (3)
>From (2):
This causes the ME to boot up in an error state, which is saved on the flash device.
Once the OS has booted, you can program the flash device.
Works on:
Montevina (ICH9M) (Oct 2007 guide) (1), (3)
Intel 3 series chipset (2)

Doesn't work on:
Ibex Peak (4)
Intel 6 series chipset (5), (6)
or presumably anything after Ibex Peak.

HMRFPO message
Works on:
Ibex Peak (4)
Intel 6 series chipset (5), (6)

Set ME disable bits (2)
From (2):
Set ME disable bits in the strap sections of the descriptor region- see ICH EDS for more info
Works on:
Intel 3 series chipset (2)

Security override strap? (2)

Temporarily stop ME thru MEbx? (4), (5)
(7) says this:
 Temporarily disable the Intel® ME through the MEBX. Power off or cold reset. -
This option is only applicable to non-Intel ME Ignition firmware.


(4), (5) says Stopping ME is not a requirement when writing to the fixed offset region.
(6) says FPT will stop ME SPI accessing automatically if it try to write data into the ME region.
Customers do not have to do extra step to stop ME if using FPT tool to update ME
region. (5) does not mention this note.

Section 8 (Update Parameter Tool) of (4),(5),(6) is interesting-
the tool will work with ME manufacturing mode bit set, and a locked Descriptor region.


References:
(1) Montevina SW/FW OEM Bring up Guide, October 2007, Rev 0.4
(2) System Tools User Guide, July 2007, Rev 0.92 (Intel 3 series chipset )
(3) Intel Management Engine, System Tools User Guide, October 2007, Rev 0.60
(4) (Ibex Peak) System Tools User Guide for Intel® Management Engine Firmware 6.0 (Corporate),
User Guide, June 2009, Revision 0.60
(5) System Tools for Intel® 6 Series Chipset Family Intel® Management Engine,
Firmware 7.0 SKU’s, User Guide, May 2010, Revision: 0.81
(6) (Cougar Point) System Tools for Intel® 6 Series Chipset Family Intel® Management Engine,
Firmware 7.0 SKU’s, User Guide, December 2010, Revision: 1.08
(7) Ibex Peak SPI Programming Guide, Application Note,
January 2009, Revision 1.3

In theory, pre-Ibex Peak chipsets should be able to take advantage of the removing memory method, which would be fairly easy to do.
The Update Parameters tool is interesting, especially if it works, but since it's a separate tool, it's not of real use.