I totally agree, but taking a child or two is at least somehow feasible. It's extremely risky and would basically take a Hail Mary attempt, but with some luck, it can be done.
OTOH, taking 52 of them is simply a logistic impossibility with the tools they have at their disposal. Those kids would absolutely need to be drugged beforehand (remember Hannah?) and it would only take one of those 104 "parents" to notice something fishy for the whole plan to disintegrate. Then, it would need to occur more or less simultaneously. It's not like that truck can tour around the Boston area and pick up the kids along the way. As soon as the disappearance of the first child is noticed, everyone in Gilead would be after them. They'd need a MASSIVE diversion to get all the guards out of their way before they'd even take off, not to mention they'd need to keep the authorities occupied with something long enough to give them a reasonable amount of time to escape. And that's just scratching the surface. I simply cannot see how it can be done.
I'll say it again, this should have happened at the start of the season, not now towards the end. I could easily see it play out as some kind of Sophie's choice, with June realizing there are far more people willing to smuggle out children than she can accommodate, and then some very difficult decisions would have to be made. It could have made for an interesting story.
He does know. He never said it out loud, but it was strongly implied several times during S2 that he's aware that Nick is the real father of June's baby. For starters, Serena told him it wasn't his baby. It can be argued that he thought she was just saying it in the heat of the argument and wasn't being serious, but his overall demeanour (hurrying to marry Nick off and send him away ASAP, for example) indicates that he knows the real story.