how about making different variants of rare cards? For example, remove the option to upgrade rare cards but do this:
rares won from the oracle, or false gods are the upgraded version.
rares won from pvp, top50 or lvls 0-3 are the non-upgraded version
rares mon from half-bloods can obviously be either
this means that you can still get these rares from t50 rarefarms, but you need to either be really lucky, or have a good deck/strategy to get the better version.
-OR-
make it so you can only challenge each person in the weekly top-50 once (obviously, if somebody new gets into the top-50, you can fight them once as well, so it's not limited to precicely 50 games). This way you will only ever get each rarefarm once per week, making them much less 'farmable'.
-OR-
make some form of rarer card that can only be obtained by, say, a different form of currency. This might be obtained through falso god wins (either 1 token per game, or 1 per mastery win, or something like that) or maybe some other way. But just make sure it isn't a card, so it can't be put into a t-50 farm. Or maybe even obtain the tokens by completing daily quests (for example: beat all false gods at least once. If you had a quest like that, you would probably have to have a way of selecting which god you face, at the cost of not getting any spins at the end or something). Or you could get the rarer cards through fighting gods with certain handicaps (like some of the ones in chris kang's trainer, or something similar).
By the way, yes i am aware that the top 2 ideas would disadvantage new players because the old players already have rares...but it does seem like it may be the best way. You can't just not deal with an issue because the solution disadvantages someone, and over time, i'm sure it will balance out eventually.