One could even argue that the polygraph benefits the person being screened, as it provides some additional motivation for them to take it seriously.
The FBI and CIA still have moles and they often times operate out of the highest levels.
They're like door locks. They keep honest people honest. They provide zero security.
Similarly, I can see how structured psychological interrogation, assisted by a polygraph, is a useful deterrent. The presence of moles doesn't negate all of its value. Just like having your house broken into once doesn't mean you'll stop using door locks.
Considering polygraphs don’t work at all, I have to imagine that an equally effective interrogation could be constructed without them.