What we're learning here is that there are actually a variety of ways to fill rust pits. A couple of things to keep in mind, though. First, it is very difficult to get all the rust out. I like to use a combination of abrasive blasting and chemical treatment, but rust works its way into steel in the form of microscopic tentacles and it is virtually impossible to get it all out without removing the pitted metal. That's not usually possible on bicycle frames and parts, so you want to be very careful to do the most thorough job you can before covering everything up with filler and paint. Shiny, clean-looking metal that was once rusty can show rust again if merely left damp overnight. Someday that rust will resurface--your goal is to kick that can as far down the road as possible. This is why the best auto restorers don't try to clean up pitted sheet metal, but cut out the affected area and fabricate and weld in replacement metal. Bicycle sheet metal is thinner than that used on autos, so welding in patches is much more difficult. Be sure to apply a phosphate treatment before painting.
On a frame, my preference would be to fill with brass, not weld. The heat of brazing also seems to help neutralize the rust you couldn't get out. Don't work with lead unless you are at least in your late 60s, or have lived a harder life than your parents demanded, though it can provide an acceptable excuse for acting stupid.
Finally, if you use Bondo or any non-metal filler, be sure to seal it well before painting or the volatiles will work their way into the paint and discolor it.