Waxing Irons will always get scratched up because most of them use aluminum as their base.
Aluminum heats up very quickly but doesn't retain heat that well. Also, its a soft metal that can easy be scratched. Any dirt particles on the board can cause scratches and any burrs on the edges can as well. Just about anything will make scratches on the base of a waxing iron.
Use a little trick I learned from a Japanese buddy of mine.
Use a scraper and scrape off as much of the existing wax as possible. Then use alcohol or base cleaner to remove any surface dirt. Instead of dripping wax on the board, rub it on like a crayon. You save wax this way as you only use what you need and when you scrape off, there's a significant difference in how much wax you save. I usually do one rub on pass from tip to tip. Then go back and rub on edge to edge. You will know what I mean when you see the patter that develops.
When heating up the wax, place some wax paper between the waxing iron and the board. Wax from the paper will melt as well and because its a different type of wax that stay on top of snowboard/ski wax and lets the iron glide easier, it will never seep wax from the paper in the base of the board and the paper will actually pick up the snowboard/ski wax instead. What it will also do is pick up a lot of the dirt. So you have to change the paper out a few times to get a board done but its totally worth it. Once you see how much dirt it actually picks up, you will always use wax paper when heating wax in the base.
After that, scrape off, as I said before, this method will not use much wax at all so you wont be scraping off much. The only downside is this method is much more time consuming. Especially the part where you rub the wax on the base like a crayon.
There's a video on youtube as well.
YouTube - #318 How To Wax A Snowboard