You hate screen protectors and can't abide by scratches. If the Adonit Jot scratched the screen of your iPad, it's hard to figure what would remedy the issue - except a screen protector, which you hate. You've backed yourself into a corner on that one.
I only see a few options (which you have do doubt considered):
1. Get a new iPad screen - about $100+, before installation; install isn't easy
2. Get a new iPad - you know the price on these
3. Get a screen protector - and here's my question: Why are you so absolutely opposed to getting a screen protector? Are you aware that, with a good installation, a screen protector is completely invisible?
4. Deal wtih it - a scratched screen won't crack or shatter any differently than a new one. This is the cheapest solution.
Also, be sure to sell the Adonit Jot on eBay. It's unmatched for fineness of line, but I'd only get one if it came with a screen protector.
Post with your thoughts. I'm sure you aren't the first to ask.