Power off the pi.

[CVL]

2) ups system... I designed a board that uses super capacitors to give 30 seconds and
    it is cheaper to build compared to battery version.   This won't work if corrupted before the capacitors get a chance to fully charge, I guess the battery can last for several attempts?

The specs say that the smallest battery of 450mAh will keep the Pi running for 8min, but poweroff is scheduled after 1min (configurable) so, yes, it should last for several shutdowns.
They have also bigger batteries which will last longer, but I got this module just for save shutdown, so the 45mAh is  sufficient.