Somewhat late to the party but a good solution I've just used goes as follows:
Buy some reasonably thick dowel (say, 10mm) and cut a length for each existing screw hole. I'd suggest the length of the screw you are using (plus about 25% extra if your door is not solid wood). Sand one end back square - this is the end that will be exposed when the dowel is inserted into the hole you are about to drill.
In your door (or frame), drill out the old holes to the same diameter as the dowel. Check the dowels for fit - there needs to be enough room for some glue around the dowel, but not too much. Sand the dowel down a bit if need be.
Now using a good strong glue (I had some 24 hour epoxy left over from a previous job), plug the holes with the dowels, being careful to push them in until they are level with the surrounding surface.
Leave to dry, for at least as long as the glue manufacturer recommends, and ideally for a bit longer - just to be sure that everything is properly set.
Now you can use your hinge as a guide to mark and drill new pilot holes in your door (or frame) before re-mounting the door.
I've just used this trick on a pair of old 2.1m solid pine doors and it works a treat.