I say, yes, the UFOs were, indeed, an advanced U.S. anti-missile system.
The hypothesis goes like this: If the U.S. had been working on the secret field propulsion system ever since the end of World War II, then it would have been reasonably developed by the 1960s.
Therefore, it would have been the ideal platform for an anti-missile system. In the case of the saucer apparently shooting a laser beam at the missile, I propose this could have been a high-intensity strobe to demonstrate that the platform could effectively target missiles in flight.
In the case of the UFOs shutting down missiles in their silos, I propose the platform was equipped with either an electromagnetic-pulse or microwave system to temporarily disarm or deactivate these missiles. But, hey, I’m not telling you anything you haven’t already contemplated. It’s all in Flying Saucers!