The French international has been linked with a move to Tottenham Hotspur and has expressed a desire to leave St Mary's this summer.
The manager told reporters: "It is difficult for him, but I said last weekend he should come back on Monday and he understood the situation and he accepted it.
"It is difficult, but he has to accept and finally he accepts. He did very good training sessions [this week] and you see the qualities and then you see why we didn't sell Morgan, because he's a fantastic player.
"When I see Morgan and I speak to Morgan, he accepted the situation, because it's his future as a football player, he knows that and that's the situation now."