I've wondered this before, it's a good question. I'd be very surprised if you can destroy someone's cognitive aspect by beating the rust out of the flame that represents it. I know it's Scadrial, but Kel wasn't able to directly affect things through the cognitive realm unless the person was mad or broken. More than that, it wouldn't make plot sense. Anyone who can get into the cognitive realm could just destroy people without resistance, switch 'em off, like they're in the Matrix.
Whether a shardblade/honorblade/nightblood can is an interesting question, but even then it just seems too overpowered.