Is Alixus as bad as Dukat, Winn, Female Changeling, Weyoun, etc.? It's a good question. Let's look at some of the main villains of DS9...
Michael Eddington - betrayed his oath to Starfleet to serve a higher cause, or so he says. What he's really doing is living out his fantasy of being a hero to people, so ego is at play here. As a villain, not that bad because while he was a terrorist and gutting a treaty, it was in defense of people who lost their homes and livelihood. Sympathetic villain in some ways, but really comes off as a douche. (It was defense... until he started actively attacking colonies outside their systems and poisoning other planets. That's when my sympathy was lost.)
Vedek/Kai Winn Adami - a power hungry, political opportunist. There are snippets that make you think she started off as someone who believed in doing good with the Bajoran religion. But I think as she rose in the ranks, something inside her twisted and turned until she was completely consumed with being the top dog. And I don't think she was redeemable, because any good that she did was ultimately to help herself. (Betraying Jaro at the end of "THE SIEGE" and trying to betray possessed Dukat in the finale, for example.) There was nothing altruistic about her. Another villain where ego was a huge factor.
Weyoun - a complex villain. He really didn't have any free will because everything he did was in service to the Founders. If the Founders decided on peace, he would have made it happen. If they wanted to fight to the last man, he would have made it happen. In some ways, he's a tragic villain, because I don't think he was truly evil. Unlike the other villains in DS9, he really had no ego.
Female Changeling - a true villain. But her reasoning for why they created the Dominion at least makes you understand and somewhat sympathize with her. However, the ruthlessness and coldhearted methodology of her actions makes her irredeemable, since there was no remorse in anything she did.
Gul Dukat - the ultimate narcissist. His entire existence has been one to make the universe view him as a heroic figure, even during his reign as head of the Bajoran Occupation. He even sold out his entire race to the Dominion so he could be elevated to be leader of the Cardassian Empire. "A true victory is to make your enemies see they were wrong to oppose you in the first place. To force them to acknowledge your greatness!" He was irredeemable on multiple levels.
Alixus - she stranded a ship full of people because she needed people to follow her philosophy of life. That's a very narcissistic mentality. She is directly responsible for the deaths of all the people who died because of their being stranded. While her goals may be noble, she never gave anyone a choice in the matter. In this regard, she's as bad as the Dominion. And she clearly had no remorse. The worst part is that none of those people wanted to leave. I'm not sure if that's more because of her cult leader behavior over the years or because those people were just too easily duped... neither scenario is good. I also find her irredeemable because not only did she have no remorse, she was smiling at the end. In a very real sense, this villain WON... her little community still kept going willingly, even after her ruse was exposed.
In short, do I find Alixus as bad as the rest? I think I'd put her villainy 3rd or 4th place. Considering she only appeared in a single episode, that says a great deal about her.