The production writers could play up one conspiracy theory that Penny was a Government agent who was placed to keep an eye on the 4. If Sheldon could almost built an Atomic bomb as a kid, what could he , as an adult with 3 other smart friends do. There were clues in the series . Like once she became friends all her other friends disappeared. She did beat Leonard at chess so had more brains than she seem to have. She was a fighter and managed to physically fight very well too.