Realistically, you don't prevent it. At least not entirely.
Part of committing to freehand sharpening is a willingness to own the results. If one ever expects to use a knife as it was meant to be used, it's going to get scratched or scuffed anyway, probably sooner rather than later. Even sharpening with a guided system runs the risk of a stray abrasive particle scratching the blade, or the corners of the stones running over & beyond the edge bevel and gouging the blade's finish (I've done that more times than I'd like to admit).
You can game the freehanding results a bit, by committing to only buying & using blades with a finish that's easier to fix, if it gets scratched. Satin-finish blades are better for that - they can be 'fixed' by simple sanding. OR, a fix for a scratched polished blade might be to put a new satin finish on it and never worry about it again. I've done that too. And hollow primary grinds on blades are inherently less prone to sharpening scratches beyond the shoulders of the bevels. They tend to always finish better, in my experience with them.