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Yes, the name doesn't make the character. If you feel a name fits the villain's personality well, what's to stop you from using it? Using a name you like does not glorify the villain, and using a name you dislike does not devalue a good character. I don't generally like to use names that I dislike, either, but giving a villain a "good" name and giving a protagonist a "bad" name doesn't change anything about them. They are still who you make them out to be, regardless of what they go by.