Obadiah was referring to the giant arc reactor running the factory, not the mini one running Stark’s heart. But later on, when Obadiah tries to get the designs for that, Stark won’t hand them over. My explanation is that a mini arc reactor is fantastically expensive to make. Stark made his first one out of parts cannibalized from a half dozen state of the art guided missiles, so we probably talking several million per reactor. So it’s not a cheap energy source by any means, merely a small, portable one. In other words, it’s mostly useful in military applications, which Stark is trying to avoid.
In a bit of amusing geek-boy irony, that was the same argument made as to why Spider-Man wouldn’t have used his web-shooters as a hero.