That really is a good idea...I wonder how you would deal with a faction that is at full capacity, though? For instance, let's say that you have 45 active people, and two more on vacation. If those people came back, would they have to wait until someone else goes inactive?
Also, people might abuse it--say someone has a weak defense deck, and they click "inactive" when they aren't attacking. They might have to make it so that a person is "inactive" for 1 week at a time--unable to attack or defend.
Still, it would be nice--much easier to set up a fortified, well-coordinated defense.