Since you are re-painting the window sill and not going for a stained or clear finish...
Glue on a 10mm (or whatever the gyprock/sill gap is) thick timber 'shim' to bring the sill flush with the new gyprock level. Use a timber similar to what is there (ie dont use a bit of pine if it is hardwood...there are usually nice bits of milled Tas Oak in a variety of sizes at your local hardware store). Thickness of window sills is about 19mm, so with a bit of luck you can find a 10x20mm piece to use.
Use a gap filling adhesive so you dont have to muck around cleaning off the edge of the old sill too much, just roughly smooth any dags off it (Araladite, West System epoxy, or a polyurethane adhesive). This also means you dont have to worry too much about filling before you paint. Just scrape/sand off the squeeze-out and you are done.
Unless you have a nail gun, pre drill a few holes to bang some nails in to hold it while the glue sets. (things like window frames can bounce like crazy when you hammer them manually, which is not condusive to good nailing).
Expect to give it a re-sand and re-paint in about 3-5 years when the new piece of timber has (hopefully) reached equilibrium...if you are really fussy with how it looks, that is.