Okay, in considering changing or removing alignment, one needs to know what rules this would effect.
What I can think of off the top of my head is:
What other rules affects in the core rulebook and bestiary rely on and use the alignment system?
Monks, paladins, and assassins of course.
-align weapon
-Holy, etc. weapon qualities
-A significant percentage of Damage Reduction and some Regeneration
-Channel Energy
-summon monster
-forbiddance
-One possible trigger for symbol spells
-hallow and unhallow
-dispel evil, etc.
-holy smite, etc.
-undetectable alignment
-Robe of the Archmagi
-Helm of Opposite Alignment
There's probably a few more.
Don't forget the various DRs
Dr 10/good, DR 5/lawful, etc.
Mainly affects devils, demons, angels and their ilk.