if someone REALLY wants to use Protection how should it be handled?
If you REALLY want to use Protection, you bite the bullet and use Extra Effort for a power stunt. The effects of Extra Effort ignoring any limits to Power Level, you can apply as much Protection as you want.
For example, if Hal Jordan stunts Protection 18, Affects Others, Burst Area, Distracting off his main array, he could apply it to the entire Justice League plus any bystanders as long as they remained within his range. It doesn't matter that this would raise Superman's toughness from 18 to 32 as it isn't limited by power level.
The kicker? Power Stunts last until their duration expires or the scene ends so as long as Hal Jordan keeps sustaining that mega-shield, his justice league buddies get the benefits.