Mourinho gave Alli his first start since November 26 at the bet365 Stadium but replaced the England international in the second half, blaming him for giving the ball away before Jordan Thompson equalised.
Alli reacted angrily to being substituted and an unhappy Mourinho confirmed that the feeling was mutual.
"When you come out and you're digging a player out in the press, I think he needs to help him," O'Hara told talkSPORT. "What's he gaining from going to the press and digging out that single performance?
"It's just killing his confidence more. He's an investment and an asset to the club and whether he's in your plans or not, you don't want to kill his confidence so much that you totally lose him.
"I didn't like the way Mourinho dug him out and he keeps singling him out. I think Mourinho's doing a great job and he's got the team all on side but, for me, it doesn't sit right with the way he keeps digging out Dele Alli.
"Even if you're gonna push him out then just say 'you're not wanted' and 'he's not in my plans'. If you're killing his confidence and saying 'he's not for me' and you're just digging out his performance, then surely you're just devaluing the player."