I can't agree with that. BSG wasn't nearly as morally ambiguous as some people make it out to be. For all the shades of gray, in the end you knew who the heroes and the villains were meant to be, and there were a few characters who had few sympathetic qualities and whose function on the show was obviously that to be villains and represent evil. Cavil/John/One was one such character, and he was made into a super-villain by season 4; The Five (Doral) models were increasingly turned into one-dimensional villains; the writers seemed to have been trying to do something similar with Tory. And then of course there were minor characters like Thorne and the "Sunshine Boys", who were meant to represent the worst of humanity, and you really couldn't help hating their guts.
You pretty much had Bad and EEEEVIL, though (to borrow your phrase). Either a character was just horrifyingly evil, or they were like Dukat: had some possibility for good, but did a LOT of evil things, which can be argued in some cases to overshadow the good.
Helo was pretty much always portrayed as the white knight of BSG, and some other characters, like Chief Tyrol, were predominantly good. All characters could be graded by the amount of 'good' and 'evil', but the judgment would depend from person to person. I still remember the heated debates on BSG forums over characters like Roslin, Tigh, Baltar, Caprica Six, Athena, Boomer, or even Starbuck. Roslin is an interesting example as she starts off as unambiguously as a heroine, and while she always remains a person who is completely and sincerely dedicated to the goal of protecting the Human race, she becomes more and more ruthless, cold and machiavellian - and some of the actions really made me hate her at the time (he was a 'love or hate' character for fans, some people even considered her to be the real villain). But that was the point of the character's story arc, and the show eventually dealt with these issues in the last season. Overall I find her to be a great character, even though I often found her hard to like.
I've seen people make that comparison before, but really, while there are some similarities (like narcissism, megalomania, and charm that makes the characters more likable than they should be), there are polar opposites in a lot of ways. They would probably both feel insulted by the comparison with the other, and with good reasons.

Dukat would probably despise Baltar and resent being in any way compared to a cowardly, passive weakling who was repeatedly manipulated or intimidated by others and never able to form a plan of action or do anything without being prompted by someone else or forced by the most immediate circumstances. Baltar, on his part, should resent being compared to a cruel, militaristic and racist person (in contrast to Baltar, who is basically peaceful and doesn't seem to feel any prejudice for people based on their species/race) who willingly, knowingly and actively committed mass murders and numerous other crimes, and who sexually enslaved, manipulated and abused many women (something that you could never accuse Baltar of, for all his sexual escapades). I always saw Baltar as an antihero/antagonist, nor a proper villain; at the beginning, the Cylons were the villains, the ones who committed the genocide, and Baltar was just a hapless pawn who had no idea what he was getting himself into. I saw him as embodiment of human weaknesses - selfishness, cowardice, lust, desperate desire to survive at all costs, lack of backbone and ethics - which made him alternately, or simultaneously, despicable and sympathetic, but I don't think he could ever be a real villain, since he almost never took an actively villainous role; the worst things he would do were horrible blunders and spur of the moment acts committed out of panic. All this puts Baltar firmly in the "
bad man" category, but I could never see him as "
evil", due to his lack of malice or cruelty. A real villain has to be a more active, more formidable figure, someone pulling the strings, or taking charge. (The Cylons seemed to be that in the beginning; when they were watered down with time, the writers finally made Cavil into this kind of villainous figure.) Which is why redeeming Baltar was always much easier than redeeming Dukat; Baltar never knowingly committed genocide and only reluctantly ordered executions when he literally had a gun pointed at his head.
Putting in my 2 cents and not trying to diss anyone's opinion, but I don't think Dukat is a sociopath nor a xenophobe. What he is, is a megalomaniac and a racist. Re: how Dukat feels about the Bajorans... has anyone ever read the poem "White Man's Burden" by Rudyard Kipling? That basically sums up the way he felt, at least initially, towards them. The poem is pretty awful (in its message) that basically white people are surperior and are "burdened" by caring for "angry, sullen peoples/half-devil and half-child," (and I'm pretty sure Kipling wasn't being sarcastic).
Bajorians are not another race to the Cardassians, they're another species.
They are alien to each other. They are from different planetary systems.
Dukat is not racist, Bajorians are not of the same races as Cardassians.
Dukat is xenophobic.
If we're going to talk about the definition of 'race' - by your logic, humans who hate other humans because of the color of their skin etc. are not racist - because there are no such things as human 'races', it's a relict of an outdated science, and nowadays it's largely a cultural construct. Humans are like cats, they come in different colors, but biologically it doesn't make sense to categorize them into 'races'.
But how are you going to call, say, an American who hates another American because he's black? It's not xenophobia, since they are both of the same nationality. If he hates a French national and believes that foreigners should all go home, that would be xenophobia.
Racism in the context of Trek is synonymous with "specism", especially since Trek aliens are really metaphors for humans. Besides, I'd question the statement that Cardassians and Bajorans can really be considered different species, since they only seem to have superficial biological differences, and they are able to reproduce together without medical assistance. The same goes for many other Trek humanoid species. That is why I prefer to call them "races" of humanoids. The only cases where you could really argue for "specism", IMO, is when there are really significant biological differences - as between the humanoids and the Founders.
Dukat is not xenophobic, because if he was, he never would have brought the Dominion to Cardassia. The Founders, the Vorta and the Jem'Hadar are definitely very foreign and alien to the Cardassians. A xenophobe also would hate to 'mix' with foreign elements, like Bajorans or Humans in this case.
Xenophobes have an irrational fear and mistrust of foreigners (not people of a different genetic background, but foreign nationals) as well as of elements of foreign cultures, and believe that the foreigners should stay away from their country. They don't necessarily think that their country and its citizens are superior to the others; they just don't want to mix with the foreigners, and they don't want foreigners to come to their country. Cultural xenophobes are resentful of foreign languages, literature, music, film, pop culture, food, etc. "invading" their country's cultural space. Xenophobia can lead to isolationism, expulsion or mistreatment of immigrants, or ethnic cleansing and genocide. But it does not lead to invading other countries or subjugating their population, to imperialism and colonialism. This would be more likely connected to and justified through nationalism/chauvinism and racism.
People who believe that their national group is superior to others are called chauvinists (the original and primary meaning of that word). Racism is the same thing but related not to the nationality, but the genetic factors and origin. Since the old belief that people can be divided into 'races' is mostly abandoned, nowadays it refers to any case of prejudice against someone based on their ethnicity. UN conventions make no distinction between 'racial' and 'ethnic' discrimination.
Dukat's views are indeed amazingly similar to the concept of "White Man's Burden", derived from the above mentioned infamous poem by Kipling. Now, Kipling's poem and that entire concept was definitely not xenophobic. It was racist and imperialistic.