I run a Via MII-6000E; probably similar to yours. I tried a number of BIOS settings and then a number of "spare" pins on the mobo. No joy.
I finally ended up using a spare power connector, a 220 ohm resistor, a bit of wire, and a bit of electrical tape. The power connector will go to zero when in S3-suspend.
----blk connect----bit of wire---led connector
----red connect----resistor------led connector
It's an ugly hack, but it works. Led is on when running, off when power off or suspend.