I know I can remove flags from individual posts (given enough rep) but I mean to flag the tag itself. For example, there is a tag called evil for which I can't imagine any useful cohesion between various tagged posts as with, say, the c++ tag (and indeed, the three tagged posts do not have anything in common really).
If you find a tag that you think doesn't belong on the site, bring it to meta, as you've done. This will allow the community to discuss the tag and determine why it is used and if it has value.
With that said, I see no value in such a tag. A better tag might be ethics, since it's more general and applies to a specific segment of software development.
ethics has 92 questions in it. Clearly, it's the closer tag people think of when they post questions about moral or ethical right or wrongs in programming.
However, evil only has 3 questions in it, so it would be really easy to retag those 3 or remove the unwanted tag. Since only 500 reputation is needed to retag a question, this is something that you could do yourself. :)
In addition, you can flag the question itself and point out the errant tag. The flag will automatically get moderator attention whereas posting in meta requires a moderator to see the question thread. Both work, a meta question isn't quite as direct.