Is there some reason "Emilian teaches civics" would not be acceptable? Does habitual require a different form?
No, it's just an alternative that hasn't been added. The -na- form is also used for habitual actions.
I thought one would use the habitual tense in this case: "Emilian hufundisha somo la uraia."
Since "somo" is used, shouldn't translation be: Emilian teaches/is teaching the Civics lesson (or the lesson in Civics)?