You might try posting your question on the DIY board at this site. There seem to be a lot of folks there who have experience with that sort of problem.
I've never attempted the kind of repair that you are describing, but wonder if there would be any problem with the dowel idea. If you were to make a plug with a dowel, you'd probably be drilling into the end grain (of the dowel) rather than across the grain. Would that be a problem? I don't know.
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