You can always go to a good third party mechanic and have them flash car to stock if needed. You won't have to deal with dealer issues or questions IF they come up. Just remember to have your 2 bar sensor to reinstall or car may not start!
If you buy new tuner from LMS, I imagine when they load new tunes on device, they include the stock tune as well. Just flash it yourself. Your only issue is shelving out another $600 for tuner and tunes. Unless they work out a deal with you!