I like making alignment official. Giving everyone chaotic or lawful alignment when that really means "trickster" or "anal retentive" makes no sense. That's simple character role play/backstory crap. Giving everyone good or evil alignment actually DOES matter. So its nice to have rules about good-evil alignment in a game about good adventuring to go kill evil until good levels up to 20.
Well, that is mainly the reason for not outright removing it actually. Having suitable types of enemies to battle in a straightforward game without too much quibbling helps gameplay a lot. Hence retaining the capacity to have Always X alignment available is a good thing.
On the quick fix end though, the biggest offenders are mostly class prereqs and icky spells. So you have these, in order of implementation difficulty:
Simple Fix: Remove alignment requirements from most classes that don't need it for a mechanical reason(i.e. paladin has alignment tied features). Bard, Barbarian, Monk, Druid, Assassin get an out. Trivial to implement
Simple Fix +1: Rewrite classes that have alignment tied features to have alternate alignment variants, paladins of X,Y and Z show up here, releasing clerics from alignment related turning as well. Slightly harder to do, but usually it's just clone and retype.
Simple Fix +2: Rewrite spells and feats that are icky, but not otherwise inherently good/evil due to drawing on aligned forces. Most of the necromantic stuff falls under this. Clerics with completely non undead related turning powers may come into play here. This is trickier since you have to dig through a metric crapton of stuff to fix
Advanced Fix: All alignment tied matters are switched to codes of conduct. Clerics, Paladins, Druids, and other divinely inspired classes take after the code of their patron, and all 'aligned' magics are modified to work based off divine order codes of conduct instead. Most spells that have an actual difference between aligned versions may need to be rewritten to suit the new schema of tying them to specific gods/domains. Hard to implement, practically a rewrite project in itself. Potential balance issues.
Advanced Fix +1: Implement incentive/penalty system for following or disobeying your
chosen codes of conduct, beyond the binary 'lose all your powers' in play for the current state. Morale effects may be significant, as well as strength of resolve(a warrior worshipping a god is far different from a paladin or cleric, who'd be downright fanatical in comparison). Not quite as big a jump, but still tricky to implement.
EDIT: Readability.