I wouldn't even worry about it, just scrape off anything sticking up with a razor blade. The scratches don't look deep enough for p-tex to hold, it'll just fall off. If you're really want the scratches gone take it to a shop and have them base grind it.
Wax will fill up the scratches too, just don't know how long it will stay in there at warm temps.
What kind of kiteboard is that? The ones I've seen look like wakeboards, or modified surfboards for racing.