You have created a kind of iron oxide, commonly used to stain wood to create the weathered look you describe. I actually keep a jar with steel wool and vinegar in my shop for this purpose. Here is a link on how to do it.

http://www.finewoodworking.com/Materials/MaterialsPDF.aspx?id=2193

I can't imagine why it would do any harm to the boat, you might be able to bleach the stained areas to lighten. I doubt you'll be able to hide to your eye unless you elect to a partial paint job.

Eric M.