Nat's a hard character to pin down. At times, he seems like the angel on Don's shoulder, warning him against the consequences of drinking. At others—well—he's the devil who's pouring his drinks.
Here's their relationship in a nutshell:
NAT: Oh, Mr. Birnam, why don't you lay off the stuff for a while. [Nat pours another shot for Don.]
As you can see, Nat frequently says one thing and does another, admonishing Don for his alcoholism as he fuels it (for a price, of course). Business is business and all that, but is it really ethical to supply a known alcoholic? Not really.
Still, Nat does eventually ban Don from his bar, but not for the reason you might expect: he disapproves of Don's treatment of the ladies in his life, Helen and Gloria.
The most angelic thing Nat does for Don, however, is returning his typewriter at the end of the movie, likely saving his life. He didn't have to do that. Perhaps Nat has finally realized how far Don has fallen, and how he as an individual contributed to that fall.
No matter his motivation, Nat deserves all the props in the world for his last-minute save.