Having the Mega Stone disappear seems like the best option, but it still feels to me like an un-Nintendo-like thing to do. Playing your XY cartridge on a friend's 3DS that doesn't have the patch installed is all it would take to lose your Mega Stones (and how many kids will neglect to download the patch?). Nonetheless, it's still probably the best course of action. Cutting off compatibility completely would be a bummer.I was talking about the issue of compatibility with my friends earlier today and wow, this is actually a really good point. I think the likeliest option is that as the data for the items would be included in the hypothetical XY patch, then the Mega Stones would simply disappear forever, so don't do it. In regards to getting the items back, maybe the patch could include a back-up that keeps track of if you own the items or not?
Another option (that would really suck but solve all issues), is simply to not have any connectivity between XY and ORAS, with us having to transfer Pokémon via Bank instead. But as I said, that would really suck.
Speaking of "un-Nintendo-like" things to do, but honestly, this could be true and I wouldn't be surprised. Either that, or they're early leftover designs that were never removed. It never made sense to me just how similar they looked to each other.