Sure, metal replacement is warranted especially on flat panels where holes can form, especially at corners, and should be done. Sometimes metal repair is impractical, but in places like doors where you have complex shapes/intersections of panels and welds, rust can create unusual holes that are not easily repaired by sheet metal patches. I stand by my suggestion as well; certainly I appreciate the integrity of metal but in an ideal world, it can't always happen, because of complexity and cost concerns.
A poor way out? Repairs are only as good as the repairer. A well planned and executed fiberglass/bondo repair will maintain long term integrity on the cheap. Bondo that has fallen out is a sign of lousy preparation, not a fault of the material.
Reread the op's message - the first thing he suggested was a "tight budget". That says alot, metal repairs are more involved/expensive, especially if your skill level and tools can't meet the challenge.
Chris