Isak is demanding Newcastle sell him to Liverpool this week and has refused to attend training in recent weeks.
Asked about the situation, Henry told Sky Sports: "When you have a player in this type of situation at Newcastle where Isak wants to leave, it’s because he’s good that people are upset.
"When a player is playing badly and the club wants him out, I don’t see anyone crying for the player.
"We never know the whole story, but all I would say is that you cannot put yourself in a situation (as a player) where you don't come to training.
The Frenchman added: "I think for me in an ideal world, the best thing for everyone would be for him to leave.
"If (Isak) realises he has made a mistake in terms of what he has done to the dressing room, he can apologise, he can move on.
"(But) the best thing for me right now would be if he goes but (Isak) needs to apologise if he wants a way back into the club."