Yes, you will have to disable the Nether or Soul Shards, I suggest Soul Shards, the Nether offers other resources that players may need for tech tree progression. Also, UU matter can be used to produce gold, so once someone starts producing enough power they will have unlimited gold. You could disable the Mass Fab but that would once again destroy tech tree progression. Its called the Matter Fab if using GregTech, and while expensive it serves the same purpose, but takes longer to reach the point of unlimited resources from UU. Another thing that could be abused is a mob spawner to get shards of minium and a zombie farm or enderman farm. They could just transmute lots of iron and enderpearls into gold.
TL;DR: Gold based economy is doomed, go with something that can't be made automatically. I suggest ThaumCraft 3 shards and amber, the only way to get them is mining.