Posting some clear pics of the scratches would likely generate more useful feedback. Most scratches can't be buffed out by hand, unless they're extremely light. Otherwise, some sanding or other more aggressive abrasive work might be needed to clean them up. On that point, what sharpener were you using, and at what grit?
The 'fix' for the scratches will likely need to start fairly close to, but slightly finer than, the grit used to make the scratches in the first place. If the scratches were made at fairly coarse grit, a sanding sequence using wet/dry sandpaper, from slightly less-coarse, to medium, to fine and EF and polishing might be needed to clean them up effectively. It's very difficult to remove deep, coarse scratches with only fine sanding or polishing alone; would take a very, very long time. The easier alternative, obviously, is just to go ahead and use the knife, and live with the added 'character' of the scratches.
David