"I just got banned from eShop and I've never used the online functions in Sun/Moon, I just downloaded Sun/Moon from freeShop yesterday and after uninstalling the games and tickets. However, I can play online, etc. Does anyone know if they are banning for using freeShop?"
Same here. It seems it's permanent and I don't wanna ruin another 3DS. I'll just play offline and try to enjoy the game, I think we've learned a valuable lesson.
Given the two possibilities, I think the safest way is to install Moon in your untouched 2DS after release date. If you unbanned your 3DS using your 2DS files it might fuck up both consoles.
In a couple of days, when the games are out, I'm sure people will be able to share them.
I'm getting the game asap and will call Nintendo if the ban doesn't lift in 15 days knowing all the things I have to provide them.