Tom Bishop: Happy?
Nathan Muir: Seventy-four casualties, an apartment block leveled, one dead terrorist? Yeah, happy.
Tom Bishop: We have some fucked up barometer for success, don't we?
Anna Cathcart: The Scotch is older than she is.
Nathan Muir: Am I supposed to feel bad about that?
Nathan Muir: We didn't know when the Doc was going to be giving the Sheik his physical but it was our one and only opportunity to take him out. So I didn't have the usual time to butter him up. Which means we needed twice the sex with half the foreplay.
Nathan Muir: You go off the reservation, I will not come after you.
Nathan Muir: She had worked both ends against the middle for so long, the middle decided to give up and go home.
Tom Bishop: Vodka did me in, I'm comin' home.
Nathan Muir: Throw out the bottle. They know.
Tom Bishop: Fuck your rules, Nathan.
Nathan Muir: Okay, but tonight they saved your life.
Charles Harker: So, sir, you and Muir came up together, right?
Troy Fogler: Mmm-hmm.
Charles Harker: How well do you know him?
Troy Fogler: No one knows Nathan, not really.
Charles Harker: Do you trust him?
Troy Fogler: He's a man who got the job done.
Tom Bishop: She's just someone I used to get to the camp.
Nathan Muir: She gonna be of any more use to us?
Tom Bishop: Not to us.
Answer: Muir has become frustrated with the CIA as a whole - now carrying out bugging ops on trade talks so the US can sell more "toaster ovens", as opposed to the 'righteous' work he's done all his career. This is compounded when he sees that the CIA are prepared to let a man (Bishop) be killed over it, which also cements his determination to stop it. Although he has underestimated Bishop's feelings and determination to rescue Hadley, that's not really the point. He sees that Bishop is doing something righteous, 'the right thing' so to speak, and sees rescuing Bishop and Hadley as a chance to a) do something worthwhile again before he retires, b) redeem himself for past sins (sacrificing people/Hadley), and c) poetically stick it to the CIA - using their own resources to carry out the rescue mission amidst the trivial 'work' they're doing now. Muir knows that when he retires he'll be broke, but he'll be able to live with himself - he did something that was morally the 'right thing', as opposed to being the cold calculating operator he's been all his career, with that conditioning being another reason he now resents the CIA (he doesn't like what he's become). He's kicked against the bureaucrats who are doing all the wrong work for the wrong reasons. Also, there's a parallel between Bishop's feelings for Hadley and his attempted rescue mission, and Muir's feelings for Bishop (he loves him like a son or a star student). Muir certainly sees Bishop as family, and you don't mess with an Amercan's family. Muir says as much in the film with the analogy about his uncle's plough horse. The student is now teaching the master - about doing things for the right reasons (love and loyalty as opposed to death and toasters).