Reese: The only way to keep Lionel safe is to keep him in the dark.
Well clearly not since him being out of the loop has resulted in him doing his own investigations into all the weird stuff happening and now Samaritan's actively trying to kill him. Tell him everything (you know, that a dictatorial artificial super-intelligence that sees your every move is behind everything) and he might stop doing things to provoke it.
I get the sentiment that knowing about Samaritan automatically puts you in more danger from it but that only stands if you don't know anything's happening and so don't go trying to investigate. He's past that point now.