The hedge fund shorting GE will profit from the value of GE dropping due to the bad news, it will profit from the value of GE dropping if there's an investigation, and it will profit if the accusations turn out to be true.
There's no reason to think Markopolos won't profit if the accusations are bogus, because he profits from the market reaction, not from the actual merits of the accusations. In fact, his experience in the past tells him that even if his accusations are true, they're unlikely to result in successful investigations, and if his accusations are untrue, he's unlikely to face consequences for it.
Also, whilst the people who go on CNBC to defend GE are paid to go on, they're paid a fixed salary, they generally aren't particularly incentivized to boost the stock price.