A Direct-to-metal epoxy would work as well. The body fillers I've been using (All Metal, and Contour from Eastwood for finishing) both say they work best on bare metal. If you shoot primer shortly after filling, you shouldn't have issues with rust.
Kevin 1951 Chevy 3100 work truck Follow this saga in Project Journal Photos 1929 Ford pickup restored from the ground up. | 1929 Ford Special Coupe (First car) Busting rust since the mid-60's If you're smart enough to take it apart, you darn well better be smart enough to put it back together.