Polly's kid was a baby! He won't remember a thing. I mean, yes, it's icky, totally gross, but if she stopped right then, her baby would never have any idea. Sam laid face down on a centuries-old grave and talked to dead people to try to get himself not to care. Booth let Sam down over and over. He may not have meant to, but he did. And the last time, when he was there for three weeks, before he left for good--that was the nail in the coffin. Because he held out this carrot of "See how great it could be, Sam?" And Sam fell for it. And then Booth left. He didn't intend to break Sam's heart, but the reality of it is that he did. We are responsible for the things we do even if the damage is unintentional.
And as far as the other thing goes: Polly's baby never had to try to decide whether to tell his dad the truth.