You're mistakenly assuming the SEC has laid out its case in the pleading. That would just be silly. They have simply laid out the bare bones arguments. There will be discovery, depositions, additional testimony and loads of new information as this moves along.
It's also apparent that the SEC and JB are far apart in what each will accept to settle the case. Regardless of whether the SEC filed this suit in an attempt as a negotiating tactic or not, they have laid out some pretty compelling evidence and a damning timeline. If the company were humming along profitably with plenty of working capital and didn't need to raise money, that might not be a problem. However, in JBI's case, it will likely at best make raising capital extremely expensive, and at worst, impossible.
Lastly, with JB as the major, and perhaps only person directing nearly all the company's activities, the distraction of defending this major civil suit and class action suits, as well as derivative actions, will likely result in his inability to do much vis-a-vis operations. The effects of that are likely to be felt in the process itself, but more importantly, by potential future investors in the company.