How I handle it
1> The mere fact that something is evil is not sufficient reason to attack it.
2> Good clerics in my game cast Detect Evil on their congregation regularly. They use it to detect those who might need some special counseling. Of course, if they detect a STRONG aura, the confrontation might not be so gentle, but the first step is still investigation.
3> Evil clerics and the like use Detect Good in order to pick out targets for their good-affecting spells and effects. They won't waste a Desecrate spell on a party with mostly neutrals.