There's an exchange system for most other items; giving players the ability to exchange for Emas would be a worthwhile addition. I think the way this could work is by exchanging a certain number of duplicate Friends. Since Emas are meant to be rare, I think a good number would be 100. At the regular prayer rate (5% chance of rolling a Friend), this would require 2,000 Prayers (10,000 Seal Crystals and 3,000,000 Coins). God Crystal prayers can bring this down, especially with Step-Up prayers and the occasional discounted Prayer, but it would still take a while to reach that number. Regardless, the dev team can set the number at whatever they feel is appropriate.
Obviously this wouldn't work if player were required to hold all the dupes in the Friends tab, so there could be a new tab on the Prayers tab where players could add the dupes, and it would slowly build up to the number needed. Another stipulation could be that players cannot add a brand new Friend to this exchange, i.e., if a player has never rolled Mokou before, they cannot add the first Mokou they roll to this exchange.
This wouldn't replace selling dupes; players could still sell any Friends (including brand new ones) for coins, spirit points, and tokens. However, they would not be able to sell them AND add them to the exchange pool. They would have to choose.