Dragon #101 is September 1985 - a decade after D&D's original publication, and over 25 years ago.
And alignment had been questioned before then. And not all versions of D&D have mechanical alignment of the same force as AD&D or 3E (eg B/X, and I believe OD&D, is less definite on exactly what, if any, the mechanical meaning of alignment is - to the extent that in an early White Dwarf Lewis Pulsipher was advocating the introduction of rules to make alignment more mechanically significant).
Not having Alignment in the game is one thing. A small step from RAW.
Not having Paladins subject to an External-to-the-Player code is a much bigger step away from RAW. Letting the player decide on his power source's morality IMO means you're turning your game away from Gamist/Sim to Dogs in the Vinyard style story-creation Narrativism.