There is a thread on BGG talking about this also. One suggestion was a drafting approach whenever there is a conflict it swaps and whoever's turn it is gets the contested card.
If you check the downloads there are new versions of the starter decks that can all be made up at once from the Core box.
In general the conclusion has been that you hope your friends buy a Core set also
In many ways, specially with the alternate mages, you're never going to be able to cater to every eventuality with a single set - like Beastmaster vs Johkari BM - I mean you know you want to try it out, but there just aren't enough cards...
The spell tombs are the most common approach from the sounds of it, but there are a couple of threads that suggest you get more cards overall, the extra markers etc with two Cores.
With the new 6 player mat coming out along with some other cool new toys, I'd suggest playing with the base set for a while, grab spell tomb 1 if you need some base cards and see where you get to...