Maybe someone who's followed the comics more closely can chime in, but didn't Stark's company fail and he restarted from scratch?
Anyways, in the video was slightly backwards, you want to do as vxicepickxv mentioned above and buy when Luthor is defeated, because that's when the stock price will be low. Realistically though, Luthor's company is a resource he'd want to continue to use, so he'd have systems in place to isolate it from him and prevent the company from sinking when he does. Since the good guys generally play by the rules, they can't do anything against the company itself.
In contrast, when villains, the government, or whomever goes after Stark, his company is a prime target, thus significantly hurting the bottom line. If threats to the company weren't an issue Stark's would be the company to invest in for the long-term because of the energy tech. Can you imagine if the oil-economy were replace with the arc reactor/repulsor economy? That's HUGE business for Stark - just think of all the money "Big Oil" has today, but condensed down to 1 company.