I've been mulling this over, and seeing the amount of growth between v.1 and v.2, I have a thought for v.3. Change Protection from [Alignment] and Magic Circle Against [Alignment] spells into simply Protection from Malice and Magic Circle Against Malice. That way, it provides the spellcaster with a simple streamlined protection spell to use and not have to distinguish from other protection/magic circle spells.
Similarly, instead of Smite Evil, why not just Smite Foe. I mean, if a Paladin accidentally smites a non-evil character, that should fall more to roleplaying than mechanics.