I have a Gigabyte GA-X79-UD3 motherboard and when I activate VT-d in the BIOS, I no longer get sound.
What can I do to avoid this problem?
Intel VT-d is "Virtualization Technology for Directed I/O" (IOMMU), used for re-mapping devices to virtualized guests. From your question is not clear your situation but I guess you have nothing to do with virtualization, so keep VT-d disabled.
In case you do virtualization and re-mapping soundcard to the guest, it's correct that soundcard has been unbinded from the host.