By now there is somewhere a page that lists the known boards with 890FX chipset that have the necessary BIOS support to use the IOMMU.
One of them is the Asus Crosshair IV Formula, which I'm thinking of using for my own little project.
I have gigabyte board too but have no problems with IOMMU. on boot up I get IOMMU GART and a quick search brought up this site. The bios has something it calls virtualisation but it doesn't seem to make any difference on Linux it may in other operating systems.