I have this issue too.
At my dojo we generally start off with a calisthenic type work out so I'll track that under calisthenics rather than martial arts for a more reasonable estimate.
For the rest of class, it depends on what we're doing. If it's just basic line drills or katas or something, to me that doesn't seem any more than just walking for a half hour so i'll try to align the calories burnt with that - so i don't necessarily track the time i'm at the dojo, i track it as martial arts but adjust the time to match what i think a more realistic calorie burn is (so if counting all your time is important to you, then this might not work). But if it's a sparring class, you could be burning that much in a half hour or so...
i do tend towards under estimating, and there's still a lot of guesstimating. hope this helps!