Baldur's Gate : The Sword Coast Chronicles : NWN2 Persistent World

‘Alignment’, if my memory serves me correctly, initially came from the wargame ‘Chainmail’ which was the precursor to 1st edition D&D. ‘Alignments’ were as much individual armies as Orks, Spess Muhreens, and Tyranids are in current WH40K. Thus, in much the same fashion as Tolkien’s ‘Lord of the Rings’ was a fight against a literal Good and a literal Evil, D&D from its birth had Good and Evil, Lawful and Chaotic as palpable divine forces which would wage open war across the face of creation.

When I was DMing in PnP, I decided to avoid the whole issue by a houserule separating issues of modern morality and D&D alignments by first renaming the alignments (in order to further separate them from moral ideals), and then preventing the players from choosing their own. Good became ‘Hallowed’, Evil was ‘Accursed’, Lawful ‘Axiomatic’, and Chaotic ‘Anarchic’.
The players got an alignment based on their class, divine spellcasting, and racial lore restrictions.

For example, paladins were ‘Hallowed Axiomatic’ automatically, aasimar were ‘Hallowed’, tieflings were ‘Accursed’, and clerics took on the specific divine alignments of their respective deity. In that respect, whether or not the character wanted to take a part in this overarching divine war for dominance, they were nevertheless embroiled in its conflict simply for existing as an actor in the grand stage of things. Most were Neutral, were they saints or cads in the way they behave.

I was looking to kill two birds with one stone in that respect. Plenty of class abilities, spells, (and when 3.5 rolled around) damage resistances where based on the alignment system, and by extension, influenced the balance of the game. Likewise, I hoped to avoid spending an entire evening arguing about whether or not burning down an orcish orphanage was a ‘good’ or ‘evil’ act.

Under such system, one could be both an aasimar paladin and a genocial maniac (if that made sense for the doctrine of the deity), or a tiefling warlock with a heart of gold who would only use their dark powers to put a smile on everyone’s face. Issues of personality were based on how well it was acted in-character, rather than a simple slot on the character sheet.

Of course, this is just how I, as a single DM, decided to handle the alignment system. In my opinion, trying to mesh D&D alignments, and the overwhelmingly extensive philosophy of morality and ethics – all into one neat ball – is a fool’s errand. Seem Gygax had the same opinion, in him saying “I am not going to waste my time and yours debating ethics and philosophy”.

tl;dr: As far as I see it, ‘Alignment’ and ‘morality’ are two separate beasts in D&D. DMs probably have better things to do, like progressing a plot, than getting tangled up in that mess if it is brought up. By that extension, why even bring it up? WHY!?