Oh I know, yes, but that was different - that was a Gyarados, though, and Selena/Calem (whatever) made it a point to say he must have bonded with it sufficiently to achieve Mega Evolution. This would be different; Maxie and Archie originally lose control of the legendaries, immediately, without ever 'owning' them as a Pokémon.
As I say this, I've changed my mind a bit, though. I mean, Ghetsis technically controlled Kyurem in B2W2, so something of the sort could easily happen with ORAS, with the respective Team Leaders Mega-Evolving the legendaries.
I would still prefer it to be a form change, but really anything is possible here.