I have exactly the same issue. A very expensive SCSI Raid and an Atto UL5d which I need to use on an iMac 5k. I haven't found any other cards and I don't want to take the risk buying an PCIe to Thunderbolt chassis without the hope that it will actually work. Unless a 3rd party writes the drivers for it, I don't think there is much hope.
I had the system working fine on Lion - haven't tried mountain lion yet.
The next issue is that if you take the risk and replace the Raid with a thunderbolt raid, you then read that Intel might perhaps discontinue Thunderbolt because it hasn't taken off so much on Windows PC. Does that mean a Thunderbolt Raid purchase now and a future Raid purchase after Thunderbolt? I don't like purchasing Raids. 😟