An alternative for filling rust-pits is knifing putty. I think it is really intended for scratches, but it works OK for pitting and can be used straight out of the tube without mixing. It's more like a very thick paint than a hard-setting filler.
It is one of those things that has many names, knifing putty, stopper, glazing putty (and that last one can really cause confusion...)
You can get Holts Cataloy from Halfords, though I have a huge tube of something else picked up at an autojumble that seems rather better.