They've indicated that they're going to try and reconcile Burnham's existence, the Spore Drive and the military/political situation with the Klingons with what we know of TOS. Beyond that, all bets are off. They've demonstrated in no uncertain terms a certain lack of focus on the canonical minutia of Star Trek, judging by the easter eggs and various references in Discovery so far (e.g. Lorca's pet tribble, the horta in his lab, etc). They've given NO indication that they were specifically focusing on Balance of Terror as an episode, and even if they had -- which they didn't -- it would only be the third time in Trek's history that particular episode was used for inspiration (because it was fucking awesome!) and the third in a row to fail to address that particular contradiction. Not saying that can't. I'm saying that they won't. Because they have better things to do, because there are literally thousands of things they need to worry about relative to Discovery's internal continuity before they can afford to start worrying about continuity with something that was filmed 50 years ago, at a time when half of Star Trek lore wasn't even fully developed yet. Maybe you could write a letter and get the guys from Star Trek Continues to do an episode about it? Either way, Discovery is not a fan film, and they have much bigger fish to fry.