The Eldrazi are portrayed as horrific beings of destruction. At the same time, they are not mindless, but rather operate on a completely different moral axis.
"Have you ever killed insects nibbling at your crops? I think that's what the Eldrazi believe they're doing to us." — Shrivel flavor text
The game has also been retoolingsome of the Too Dumb to Live of its goblins into Blue And Orange Morality about personal well-being.
Hell, the colors themselves: Every color (of five) has two enemies and two allies, leading to some inherent blue-and-orange-ness:
White is law and order. But Light Is Not Good, since white can also become oppressive. White's allies are green and blue; white's enemies are black and red.
Blue is interested in knowledge and rational thinking. But this doesn't mean it's necessarily good, since acquiring knowledge can lead to ethical issues; blue's allies are white and black, while its enemies are red and green.
Black turns inward, toward the self. Remember that Dark Is Not Evil, since it's still possible to do good while pursuing self-interest. Black's allies are red and blue, where as it's enemies are white and green.
Red is the color of freedom, emotion, and destruction. Red sounds inherently blue and orange, since freedom is generally considered good while destruction is usually viewed as negative. And of course, emotions go all over the map. It's allies are black and green and it's enemies are white and blue.
Green is the power of nature and lives on instinct. Green is really the ultimate Blue/Orange color, since nature doesn't care at all about artificial moral codes but rather lives by the law of the jungle. Green's allies are red and white; green's enemies are blue and black.
Color pairs usually emphasis what the two colors have in common. This goes well for allied pairs, since they're allied for a reason. When dealing with Enemy pairs, things can get a bit funky, and usually result in a wide variety of philosophies, often hypocritical in execution.
Phyrexia seems to be getting retooled to this from their former role as more or less Omnicidal Maniacs. Though incredibly cruel and ruthless from a human perspective, Phyrexians earnestly believe that flesh-based life is deeply flawed at best, if not totally evil, so they're really doing people a favor by killing or converting them in horrifying ways. They're also growing factions along the color lines above:
White Phyrexia follows a scripture talking of the inadequacy of flesh, and the unity of all. It considers skin a barrier to unity, and flaying is treated as a purification rite.
Blue Phyrexia is constantly trying to improve themselves... by taking apart other beings to learn how their few good traits work.
Black Phyrexians fight among themselves, each of them trying to prove that they are the strongest and should get to run Phyrexia their way.
Red Phyrexia is finding itself filled with confusion, the ideals of personal freedom from red mana in conflict with the hive-like nature of Phyrexia.
Green Phyrexia seeks to change, grow, and approach perfection through an accelerated form of natural selection.
In the second Yu-Gi-Oh! Duel Terminal storyline, Gishki Noelia was shown acting cruel and evil on some cards, but good and benign in others. The art of "Aquamirror Illusion" and "Aquamirror Cycle" suggests she forced Gishki Emilia to transform into "Evigishki Gustkraken" against her will, and she seems to have had orchestrated the alliance with the Evilswarms due to cards like "Trial and Tribulation" and "Creeping Darkness" which resulted in her being turned into Gishki Psychelone. On the other hand, she is seen comforting crying children on "After the Storm" and protecting them in "Spell Wall". (Possibly, she was committing evil in order to accomplish what she believes will bring about greater good, in which this Trope may apply.)