Just tap the book on the table a few times then dust off anything that remains with the nearest napkin (or blow on it with the built-in can of compressed air in your chest).
Another thing you could try is not eating over top of your books. I read while I eat too and I put the book off to the side. Food doesn't fly over there unless I eat like a wild animal.
If you're eating exceptionally messy food, like a rack of BBQ ribs, or a whole turkey leg, or spaghetti with your hands, or live squirrels, just don't read while you eat (or accept that you'll trash what you're reading).
You could also save up and buy a Kindle or something.
And I hate to point out the obvious but if you find using a pencil leaves pencil marks, try something pointy that isn't a pencil... I mean, it shouldn't be a surprise to you that your pencil is working as designed and drawing lines...