Sorry for the thread necromancy, but I felt its better to continue this one then to make a new one ok?
When you really read the spell description of Detect Evil, you will notice that there is no reference to alignment. You notice "evil auras", but what is that?
And now let's look at the basic defination of alignment:
Alignment is a tool for developing your character’s identity. It is not a straitjacket for restricting your character. Each alignment represents a broad range of personality types or personal philosophies, so two characters of the same alignment can still be quite different from each other.
In addition, few people are completely consistent
So IMO having an evil alignment does not make anyone evil. Instead DM can choose whether anyone has "aura of evil" case-by-case basis. Like for intance committing yourself to pure evil, such a belonging to an evil cult could make you evil. Also thinking evil things while the spell is in effect could make you evil at that moment (even though you're neutral).
But no one is consistently evil, only few people. So even though players use Detect Evil on NPC which is somewhat evil according to some lax identity tool, there is no reason that the person is evil at that specific moment. Even the rules say so.
If CE assassin is drinking a beer in a tavern, what is evil about that? Where is the evil at that moment? "You sense presence" of evil... nope... "You sense evil aura"... where is assassin's aura? Nobody has aura, expect by spell or by specific class or prc etc.