Yes, CPs above 5000 could unbalance the meta. But in general, I don’t think Mega forms will do that, and here’s why:
While people are (somewhat rightly) focusing on how crazy powerful Mega Mewtwo, Rayquaza, and the primal forms of Kyogre and Groudon) are, I think what we’ll see first, and for some time, are the lower CP ones (lower being relative here). Mega Blastoise and Mega Venusaur would be very competitive at the top of the Master league, right now, coming in at just under CP 4000, per the page at Pokemon GO Hub (https://pokemongohub.net/post/speculation/mega-evolution-concept-pokemon-go/) There’s no reason they couldn’t come into play now, and Kyurim Black and White (see below) would be a bit stronger than these additions. That’s where I see the Master League heading over the next several months - I don’t foresee Mega Mewtwo anytime soon, but rather, Kyurim Black and White entering, and various mega forms coming in to keep them in check. Mega Gardevior, for example, is a nice foil to them at CP 4513 (per Pokemon Go Hub referenced above), and Mega Aggron, Mega Scizor, and Mega Aerodactyl could all also be good counters (perhaps this is why Aerodactyl is now available from ‘Hatch an Egg’ and not just the far more time consuming ‘Win 5 raids’).
Of course, we still don’t know the mechanics for Mega forms. Can you have more than one (probably not)? Do you need an item, or a quest to make it happen? Can you use said item with one pokemon, then switch it if you get a better/different one? All questions that need to be answered, which makes this an interesting time to be playing.
In the tease for Kyurim, Niantic mentions that it has a ‘special power’. Based on the way it worked in the MSG, my suspicion is that this ‘special power’ is the ability for Kyurim to combine with either Reshiram or Zekrom and make Kyurim Black and Kyurim White. This may require an item, or it may be innate. It may happen the day you get your first Kyurim, or it may take several months to come up. It may re-randomize IVs, or it may average them, or it may take the better overall, or the better of each, or just the ones from Kyurim or the Reshiram/Zekrom. We don’t know what it will do, or how it will work, and we can’t make informed decisions until we do.
Now, I’m not advocating that we do nothing until the full picture comes out, but here’s what I’m doing. I’m not trading or transferring any of my Tau trio (Reshiram, Zekrom, Kyurim) until I have a better idea of what’s happening. I’m working to get good versions of each one (not overly successfully, unfortunately), like we all are.
Finally, I could also see, with this influx of high CP pokemon, a new league forming with a CP cap of 4000 or 4500, or possibly even 3500 and another one higher up. This will give us a whole new set of optimizations to consider, and create a new structure for the meta.
Take home - the first Mega forms and Kyurim Black/White will probably be fairly well balanced, and will shift the meta to new stuff. We probably won’t see the crazy high CP stuff for a while, if at all. So chill out, and stay tuned to see where the game goes next.