This bug has gotten some attention. http://www.linux-hero.com/rant
/explanation-ubuntu-hard-drive-wear-and-tear

Is it, like suggested in the comments, /etc/acpi/power.sh that controls this? 
It reads /etc/default/acpi-support and in my config it says;
# Switch to laptop-mode on battery power - off by default as it causes odd
# hangs on some machines
ENABLE_LAPTOP_MODE=false

So, is this related to the acpi-support package, or is it more related
to gnome-power-manager?

If acpi-support, making a patch that adds an option to the defaults,
"LAPTOP_MODE_HARDDRIVE_POWER=X" with an explanation of the issue should
be trivial, and a great bug for mentoring someone new. If a problem with
gnome-power-manager, perhaps it's a bit more tricky.

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hard disk power management after resume
https://bugs.launchpad.net/bugs/137420
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