It is an important distinction that you draw. No application should be saying "nothing has happened for a while, time to suspend". Rather it should be able to say "something is happening, don't suspend just now".
However "should be" != "is"
The Power Management Preferences on my Gnome desktop have an option "Put compute to sleep when inactive for: ....". Assuming that text is representative of what is actually done, the g-p-m seems to be acting in exactly the wrong way.
I read the original lkml thread, and a big part of John's apparent motivation was to be able to intervene when g-p-m explicitly tries to put the system to sleep. Apparently a dbus API is coming but until then.....
It is actually fairly easy to interfere with g-p-m. Simply create an empty file and bind-mount it over /sys/power/state. Then when g-p-m tries to suspend the system it will write to the file instead. Some daemon can watch the file and when "mem" appears in it, check that nothing else wants to keep the system up, and only then write to /sys2/power/state (assuming sysfs is mounted at /sys2 as well).
It is a bit ugly, but it should allow effective prototyping of a sensible suspend manager until g-p-m comes to the party.
(and if there are any g-p-m developers listening who want to tell me that I'm completely wrong about g-p-m, I'd love to hear the details, thanks!)