Here's an idea, put all the units from the planet in a bag, raise the bag 12 inches from the board, dump the bag of units on the planet, what ever lands in the planet circle stays, all other units that fall outside the planet are removed.
the action cards seems vague, but I would think it is up to the person that won the action card to decide which units to remove.
Other than that, the cubes idea sounds good, 1 cube per unit remove the lowest ranking unit of that color first.
Plague Cure Withheld!
A horrible disease devastates a planet. Select a planet and randomly eliminate five units (including Sentinels). Surviving units are returned to the planet.
Planetary Civil War
A civil war erupts! Select one planet and randomly remove half (rounded down)of all units on that planet.