I hope they can pull it together. I have a feeling that 343 was constantly reassuring MS higher ups them that everything was great and on track, but maybe Phil and company only knew what it really looked like in gameplay form just prior to the reveal. At that point they felt they were already committed to showing it, the internet backlash ensued, and MS management decided to step in and let 343 know they were going to be overseeing things closely through release.
Microsoft has a very hands off approach right now. They can't micromanage all these studios at the rate they're expanding. While Obsidian, InXile, Ninja Theory, Double Fine, Playground etc can all be left alone because they've waded through the rough waters on their own, 343 is a different beast. They were built under the most corporate version of Xbox 1st party. They were constantly guided by execs. They're the only studio I can identify who's not led by a creative. Maybe they're struggling to handle this transition of creative autonomy under their current leadership. They just changed major creative leads last year.
To be fair, it's possible the new leads who were brought in weren't handed the smoothing sailing ship and still anticipate getting it in order by launch. I'm willing to wait and see before freaking out further.