It can mess up the threads if you do a sloppy job. But it shouldn't be too bad, if the top threads are a little bit chewed up, just screw in the bolt as you normally would. It will take a lot more effort, but since the fork is aluminum, it should re-thread it fairly well. You might not want to do a whole half inch though. Maybe like a 1/4 inch, and then a 1/4 inch spacer. If you really want to do the whole half inch, I suggest making sure that you would still be able to thread the bolt in enough once it's cut (before you cut it obviously). If you think you might not do such a great job, take it to a machine shop.
And just so you know, it's a fairly long fork tube. I need to run spacers on mine, and I have a full size SCS. You might need to cut half an inch and still use a 1/4" spacer.