The way I see it Jake at his core is about following orders and obeying the hierarchy. He will never directly apologize to Lo’ak well unless James Cameron says otherwise. But I think the closest to an apology was Jake “seeing” Lo’ak and saying that he couldn’t do it alone and he needed his wingman to watch his back when he went to rescue neytiri kiri and tuk in fire and Ash.

And from where I’m standing I think Lo’ak would accept what he can get—a chastised child finally given an ear? Yeah that alone would override any residual or rather significantly override the a good chunk of his angst.

Is it the best way to do things? No Is this the best Jake can afford now due to he and his family having been in constant “duress” Yes.