Given that in (especially older) D&D positioning, Good isn't necessarily about good, but about hurting and beating back Evil*, paying evil unto Evil, it's easy to see the outsider's view that they're not actually ideological forces, but opposing teams, one of which is admittedly full of bad guys and the other full of bad guys justifying themselves.
At which point, you obviously don't want Evil to win, but there's a reasonable fear that once Evil is gone, 'Good' will start rationalizing killing Neutral next.
*And even with 3.5 definitions, the example character for Lawful Good, which 3x treats and implies as best good, is Allhandra, a paladin who fights evil without mercy. Because mercilessness is clearly a quality of someone who respects the life and the dignity of anyone.