To your last question: haha, of course not. To the former: he pays some lip service to this idea in order to convince Andrea to investigate the ALOP, but one doesn't QUITE get the sense that this is his greatest problem with it.
ICYMI, here's Alex's post on the episode:
It Takes A Village To Run A Village
Wayward Pines takes us backstage to convince us that there's a method to Dr. Pilcher's madness -- and mostly succeeds.
First of all HA! Second, isn't that the case because his parents weren't actually there? They're outside the Dome someplace, so they're presumably not cocooned.