I would leave it, I like when my tools have that old partial paint finish...
But if I were you, I'd go over it with a coarse scotchbrite pad or wheel to take off the loose rust and the paint, and then let it brown (going over it again once in a while to smooth the browning). If you want to accelerate the process, take it outside and put a little bleach on it, and then scotchbrite again. Gives that nice smooth rust finish.