Well, I certainly didn't encounter assumed dislike of aliens, but then most of my characters are nonhuman, and the only one who isn't (a cyborg) is Republic side.
My Sith Sith seems to mostly have the same dialogue options as humans, however. And he certainly never had to act like he was prejudiced against non-human non-Sith. Let's see, after Chapter One, so Taris (the only option you have to not fight the Republic Cathar--and Republic in general--is to decline the quests; you can't say it's great that the nekghouls are training as Jedi, but you can certainly recruit them rather than wiping them out, and everyone but the humorously vicious and incompetent Thana Vesh is pleased if you do), Quesh (...is it somehow bad to fight the Republic and Republic-aligned Hutts?), Hoth (again everything there is against the Republic, and unlike Taris it's "This is a Chiss world and the Republic is unwelcome," rather than, "That jawless idiot Malak decreed this world will become a ruin and so it must stay one!"), Belsavis (very morally awkward world...for the Republic. Marvelous for Imperials who care about morality at all), Voss (again, I'm not sure what you're talking about--yes, Darth Serevin isn't interested in the truth, but that doesn't mean you have to not be, and the Republic respects the Voss even less than Serevin does), and Corellia (which the Empire is trying to conquer, and, yes, if you take the non-class missions it assumes you are too). The difference is that starting somewhere in Chapter Two the Republic and the Empire are openly at war.
Is your objection that you can't act like the Republic isn't at war with you? Because as far as the non-class missions go that's all I can figure out for "choose good over orders." On Hoth if you rescue the Ortolan engineer from the Republic rather than choosing the "we just need the reactor, not you" option, the mission-giver's reaction is, "Oh good, I was hoping they'd stay on." Or that you have to deal with mission-givers who are open racists, even though you don't have to be one?
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My Sith Sith seems to mostly have the same dialogue options as humans, however. And he certainly never had to act like he was prejudiced against non-human non-Sith. Let's see, after Chapter One, so Taris (the only option you have to not fight the Republic Cathar--and Republic in general--is to decline the quests; you can't say it's great that the nekghouls are training as Jedi, but you can certainly recruit them rather than wiping them out, and everyone but the humorously vicious and incompetent Thana Vesh is pleased if you do), Quesh (...is it somehow bad to fight the Republic and Republic-aligned Hutts?), Hoth (again everything there is against the Republic, and unlike Taris it's "This is a Chiss world and the Republic is unwelcome," rather than, "That jawless idiot Malak decreed this world will become a ruin and so it must stay one!"), Belsavis (very morally awkward world...for the Republic. Marvelous for Imperials who care about morality at all), Voss (again, I'm not sure what you're talking about--yes, Darth Serevin isn't interested in the truth, but that doesn't mean you have to not be, and the Republic respects the Voss even less than Serevin does), and Corellia (which the Empire is trying to conquer, and, yes, if you take the non-class missions it assumes you are too). The difference is that starting somewhere in Chapter Two the Republic and the Empire are openly at war.
Is your objection that you can't act like the Republic isn't at war with you? Because as far as the non-class missions go that's all I can figure out for "choose good over orders." On Hoth if you rescue the Ortolan engineer from the Republic rather than choosing the "we just need the reactor, not you" option, the mission-giver's reaction is, "Oh good, I was hoping they'd stay on." Or that you have to deal with mission-givers who are open racists, even though you don't have to be one?