What gauge is the barrel made from?
If the rust recurs & it likely will, rather than Repaint try seasoning the bare metal areas with oil.
When I had my BDS (Big Drum Smoker), I was starting to get some spots after about nine months, and Rocky told me to sand them down, put a rust resistant primer on the spots, then spray paint with a high heat black grill paint. Worked like a charm. Thing looked brand new on the outside. I never cleaned the inside, except for the ashes. Cooked on that barrel for over two years, before I bought my first pellet grill in 2009. I don't know any thing about steel gauges, but Rocky's 18 inch weighed over eighty pounds. Cooked every thing around 225 to 240 grill temp, and boy, did it get smokey food, so much so, my bride said, "Cease and desist"! And, of course, I did!!
OD